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Information on EC 2.7.7.7 - DNA-directed DNA polymerase
for references in articles please use BRENDA:EC2.7.7.7
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EC Tree 2 Transferases
2.7 Transferring phosphorus-containing groups
2.7.7 Nucleotidyltransferases
2.7.7.7 DNA-directed DNA polymerase
IUBMB Comments
Catalyses DNA-template-directed extension of the 3′- end of a DNA strand by one nucleotide at a time. Cannot initiate a chain de novo. Requires a primer, which may be DNA or RNA. See also EC 2.7.7.49 RNA-directed DNA polymerase.
The enzyme appears in viruses and cellular organisms
- 2.7.7.7
- strand
-
single-stranded
-
fidelity
-
holoenzyme
- mismatch
- bacteriophage
- pcna
- fork
- polymerization
- aphidicolin
- duplex
-
proofreading
-
calf
- endonuclease
- thymus
-
clamp
-
misincorporation
- helicase
-
abasic
-
template-primer
- 5'-triphosphate
- dntps
-
stall
- thymine
-
error-free
- mispairs
-
anneal
-
sliding
-
uv-induced
-
incoming
-
exonucleolytic
- replisome
-
transversions
- deoxyribonucleoside
- xeroderma
- pigmentosum
- ssdna
-
deoxynucleotide
-
hypermutation
-
undamaged
-
okazaki
- dtmp
-
slippage
-
cyclobutane
- transcriptases
- dnab
-
watson-crick
-
high-fidelity
-
myeloblastosis
- aquaticus
- synthesis
- analysis
- drug development
- diagnostics
- biotechnology
- medicine
- molecular biology
showSynonyms
dna polymerase alpha, dna polymerase beta, dna polymerase iii, pol beta, klenow fragment, dna polymerase delta, taq dna polymerase, pol delta, pol alpha, dna polymerase gamma, more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
ASFV DNA polymerase
ASFV Pol X
Bst DNA polymerase
CpDNApolI
DBH
Dbh polymerase
deoxynucleate polymerase
-
-
-
-
deoxyribonucleate nucleotidyltransferase
-
-
-
-
deoxyribonucleic acid duplicase
-
-
-
-
deoxyribonucleic acid polymerase
-
-
-
-
deoxyribonucleic duplicase
-
-
-
-
deoxyribonucleic polymerase
-
-
-
-
deoxyribonucleic polymerase I
-
-
-
-
DNA deoxynucleotidyltransferase
DNA duplicase
-
-
-
-
DNA nucleotidyltransferase
-
-
-
-
DNA nucleotidyltransferase (DNA-directed)
-
-
-
-
DNA pol
DNA pol B1
DNA Pol eta
DNA pol NI
DNA pol Y1
DNA polmerase beta
-
-
-
-
DNA polymerase
DNA polymerase 1
DNA polymerase alpha
DNA polymerase B1
DNA polymerase B2
DNA polymerase B3
DNA polymerase beta
DNA polymerase D
DNA polymerase delta
DNA polymerase Dpo4
DNA polymerase epsilon
DNA polymerase eta
DNA polymerase gamma
DNA polymerase I
DNA polymerase II
DNA polymerase III
DNA polymerase III epsilon subunit
DNA polymerase iota
DNA polymerase IV
DNA polymerase kappa
DNA polymerase lambda
DNA polymerase mu
DNA polymerase X
DNA polymerases D
DNA replicase
DNA-dependent DNA polymerase
Dpo1
Dpo2
Dpo3
Dpo4
Dpo4 polymerase
Dpo4-like enzyme
duplicase
-
-
-
-
family B-type DNA polymerase
hoPolD
Igni_0062
K4 polymerase
K4pol
K4PolI
Klenow fragment
KOD DNA polymerases
M1 DNA polymerase
M1pol
mitochondrial DNA polymerase
mtDNA polymerase NI
nucleotidyltransferase, deoxyribonucleate
-
-
-
-
PabPol D
Pfu DNA polymerase
PH0121
PH0123
phi29 DNA polymerase
-
phi29 DNApol is included in the B family (eukaryotic-type) of DNA-dependent DNA polymerases
phPol D
Pol
pol alpha
Pol B
pol beta
pol delta
POl epsilon
Pol eta
Pol gamma
Pol I
Pol II
pol III
pol iota
Pol IV
pol kappa
Pol lambda
Pol mu
pol NI
Pol theta
Pol X
POL1
PolB
POlB1
polD
PolDPho
Poleta
PolH
polI
poliota
PolX
polymerase alpha catalytic subunit A
Pwo DNA polymerase
R2 reverse transcriptase
-
capable of efficiently utilizing single-stranded DNA as a template
RAD30
Saci_0554
sequenase
-
-
-
-
Sso DNApol
SSO0552
SSO2448
SsoDpo1
Taq DNA polymerase
Taq Pol I
-
-
-
-
Taq polymerase
Tba5 DNA polymerase
Tca DNA polymerase
-
-
-
-
Tga PolB
TGAM_RS07365
Tkod-Pol
translesion DNA polymerase
translesion polymerase Dpo4
additional information
DNA polymerase
-
-
-
-
DNA polymerase alpha
-
-
-
-
DNA polymerase Dpo4
-
DNA polymerase gamma
-
-
-
-
DNA polymerase I
-
-
-
-
DNA polymerase II
-
-
-
-
DNA polymerase III
-
-
-
-
DNA polymerase III epsilon subunit
-
3'-to-5' proofreading exonuclease of the holoenzyme
DNA polymerase III epsilon subunit
-
3'-to-5' proofreading exonuclease of the holoenzyme
-
DNA polymerase iota
-
member of the Y-family of specialised polymerases that displays a 5'-deoxyribose phosphate lyase activity
DNA polymerase IV
-
-
DNA polymerase IV
-
DNA polymerase lambda
-
-
DNA replicase
-
-
-
-
DNA-dependent DNA polymerase
-
-
-
-
Dpo4
-
-
Dpo4
-
690931, 690974, 695225, 704514, 718837, 719283, 719650, 719817, 719836, 719841, 720575, 720577, 721665, 724266, 724354, 724363, 724387, 724705, 724739, 724740, 724744, 724745, 724746, 724760, 724845, 725350, 725361, 725374, 725377, 725385, 725390, 725439, 725702, 725713, 725996, 726028, 726077, 726358, 729272, 760580
Klenow fragment
-
-
-
-
Klenow fragment
the Klenow fragment of Escherichia coli DNA polymerase I houses catalytic centers for both polymerase and 3'-5' exonuclease activities
PH0121
ordered locus name of DNA polymerase II large subunit
PH0121
ordered locus name of DNA polymerase II large subunit
-
PH0123
ordered locus name of DNA polymerase II small subunit
PH0123
ordered locus name of DNA polymerase II small subunit
-
Pol gamma
-
-
-
-
Taq DNA polymerase
-
-
-
-
additional information
-
the enzyme belongs to the DNA polymerase Y family
additional information
-
the enzyme belongs to the DNA polymerase Y-family
additional information
-
the enzyme belongs to the Y-family polymerases
additional information
-
the enzyme belongs to the Y-family polymerases and is a member of the RAD30A subfamily
additional information
the enzyme belongs to the Y-family polymerases
additional information
the enzyme belongs to the Y-family polymerases
additional information
the enzyme belongs to the Y-family polymerases
additional information
the enzyme belongs to the Y-family polymerases
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
mechanism of exonuclease activity
-
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
mechanism of exonuclease activity
-
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
mechanism
-
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
mechanism
-
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
mechanism
-
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
mechanism
-
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
mechanism
-
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
mechanism
-
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
mechanism
-
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
mechanism
-
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
mechanism
-
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
mechanism
-
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
mechanism
-
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
overview: basic mechanism of replicative DNA polymerases alpha and delta
-
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
overview: basic mechanism of replicative DNA polymerases alpha and delta
-
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
mechanism of polymerase translocation along templates
-
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
mechanism of polymerase translocation along templates
-
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
binding mechanism
-
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
binding mechanism
-
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
reaction mechanism
-
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
reaction and kinetic mechanism, overview
-
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
nucleotidyl-transfer reaction mechanism, intermediate structures and energy profiles, overview
-
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
modelling and simulation of the reaction mechanism, detailed overview
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
mechanism
-
-
2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
-
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
nucleotidyl group transfer
-
-
-
-
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SYSTEMATIC NAME
IUBMB Comments
deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (DNA-directed)
Catalyses DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time. Cannot initiate a chain de novo. Requires a primer, which may be DNA or RNA. See also EC 2.7.7.49 RNA-directed DNA polymerase.
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CAS REGISTRY NUMBER
COMMENTARY
9012-90-2
-
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
2'-deoxyguanosine triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
Products: -
?
2-hydroxy-2'-deoxyadenosine 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase eta incorporates 2-hydroxy-2'-deoxyadenosine 5'-triphosphate opposite template G during DNA synthesis
Products: -
Products: -
?
5-ethynyl-dCTP + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
Products: -
?
5-ethynyl-dUTP + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
Products: -
?
5-phenyl-dCTP + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
Products: -
?
5-phenyl-dUTP + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
Products: -
?
5-vinyl-dCTP + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
Products: -
?
5-vinyl-dUTP + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
Products: -
?
5-[(1E)-3-[(4-[[(5-azido-2-nitrophenyl)carbonyl]amino]butanoyl)amino]prop-1-en-1-yl]uridine 5'-triphosphate + DNAn
?
5-[(1E)-3-{[(5-azido-2-nitrophenyl)carbonyl]amino}prop-1-en-1-yl]-2'-deoxyuridine 5'-triphosphate + DNAn
?
7-deaza-dGTP + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
Products: -
?
7-ethynyl-7-deaza-dATP + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
Products: -
?
7-ethynyl-7-deaza-dGTP + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
Products: -
?
7-methyl-7-deaza-dATP + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
Products: -
?
7-methyl-7-deaza-dGTP + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
Products: -
?
7-phenyl-7-deaza-dATP + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
Products: -
?
7-phenyl-7-deaza-dGTP + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
Products: -
?
7-vinyl-7-deaza-dATP + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
Products: -
?
7-vinyl-7-deaza-dGTP + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
Products: -
?
8-bromo-dATP + DNAn
?
Substrates: dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2-deoxyribofuranosid-5-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
Products: -
Products: -
?
8-hydroxy-2'-deoxyguanosine 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase eta incorporates 8-hydroxy-2'-deoxyguanosine 5'-triphosphate opposite template A and slightly opposite template C during DNA synthesis
Products: -
Products: -
?
Cy3-dATP + DNAn
diphosphate + DNAn+1
-
Substrates: systematic determination of the single-turnover incorporation kinetics of all four native nucleotides and a set of Cy3-labeled nucleotides by the Klenow fragment of Escherichia coli DNA polymerase I
Products: -
Products: -
?
Cy3-dCTP + DNAn
diphosphate + DNAn+1
-
Substrates: systematic determination of the single-turnover incorporation kinetics of all four native nucleotides and a set of Cy3-labeled nucleotides by the Klenow fragment of Escherichia coli DNA polymerase I
Products: -
Products: -
?
Cy3-dGTP + DNAn
diphosphate + DNAn+1
-
Substrates: systematic determination of the single-turnover incorporation kinetics of all four native nucleotides and a set of Cy3-labeled nucleotides by the Klenow fragment of Escherichia coli DNA polymerase I
Products: -
Products: -
?
Cy3-dUTP + DNAn
diphosphate + DNAn+1
-
Substrates: systematic determination of the single-turnover incorporation kinetics of all four native nucleotides and a set of Cy3-labeled nucleotides by the Klenow fragment of Escherichia coli DNA polymerase I
Products: -
Products: -
?
dADP + DNAn
phosphate + DNAn+1
Substrates: activation energy analysis of the forward (DNA synthesis) and reverse (phosphorolysis of DNA) reactions catalyzed by the Taq DNA polymerase shows that DNA synthesis is strongly favored, allowing robust replication from low-energy substrates
Products: -
Products: -
?
deoxxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the phosphoryl transfer step may be rate limiting for the non-cognate nucleotide incorporation by the enzyme
Products: -
Products: -
?
deoxynucleoside triphosphate + primed M13n
diphosphate + primed M13n+1
-
Substrates: -
Products: -
Products: -
?
dPTP + DNAn
?
Substrates: i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-beta-D-2'-deoxyribofuranosid 5'-triphosphate. dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine
Products: -
Products: -
?
poly(dA)/oligo(dT)x + n dTTP
poly(dA)/oligo(dT)x+n + n diphosphate
Substrates: preferred substrate
Products: -
Products: -
?
poly(rA)/(dT)12 + dTTP
poly(rA)/(dT)13 + diphosphate
-
Substrates: -
Products: -
Products: -
?
r8-oxo-GTP + DNAn
diphosphate + DNAn+1
Substrates: relative to correct dGTP insertion, r8-oxo-GTP insertion efficiency opposite dC and dA is reduced more than 250000fold and 4000fold, respectively. Insertion of r8-oxo-GTP is less efficient than 8-oxodGTP by 700- and 4300fold opposite dA and dC, respectively
Products: -
Products: -
?
2-aminopurine-2'-deoxy-D-ribose 5'-triphosphate + DNAn
diphosphate + ?
Substrates: -
Products: -
Products: -
?
2-aminopurine-2'-deoxy-D-ribose 5'-triphosphate + DNAn
diphosphate + ?
Substrates: -
Products: -
Products: -
?
2-thio-dCTP + DNAn
?
Substrates: dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2-deoxyribofuranosid-5-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
Products: -
Products: -
?
2-thio-dCTP + DNAn
?
Substrates: dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2-deoxyribofuranosid-5-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
Products: -
Products: -
?
5-methyl-dCTP + DNAn
?
Substrates: dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2-deoxyribofuranosid-5-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
Products: -
Products: -
?
5-methyl-dCTP + DNAn
?
Substrates: dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2-deoxyribofuranosid-5-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
Products: -
Products: -
?
5-[(1E)-3-[(4-[[(5-azido-2-nitrophenyl)carbonyl]amino]butanoyl)amino]prop-1-en-1-yl]uridine 5'-triphosphate + DNAn
?
-
Substrates: -
Products: -
Products: -
?
5-[(1E)-3-[(4-[[(5-azido-2-nitrophenyl)carbonyl]amino]butanoyl)amino]prop-1-en-1-yl]uridine 5'-triphosphate + DNAn
?
-
Substrates: -
Products: -
Products: -
?
5-[(1E)-3-{[(5-azido-2-nitrophenyl)carbonyl]amino}prop-1-en-1-yl]-2'-deoxyuridine 5'-triphosphate + DNAn
?
-
Substrates: -
Products: -
Products: -
?
5-[(1E)-3-{[(5-azido-2-nitrophenyl)carbonyl]amino}prop-1-en-1-yl]-2'-deoxyuridine 5'-triphosphate + DNAn
?
-
Substrates: -
Products: -
Products: -
?
5-[N-(2-nitro-5-azidobenzoyl)ami-nomethyl]-2'-deoxyuridine 5'-triphosphate + DNAn
?
-
Substrates: -
Products: -
Products: -
?
5-[N-(2-nitro-5-azidobenzoyl)ami-nomethyl]-2'-deoxyuridine 5'-triphosphate + DNAn
?
-
Substrates: -
Products: -
Products: -
?
7-deaza-2'-deoxyadenosine 5'-triphosphate + DNAn
diphosphate + ?
Substrates: -
Products: -
Products: -
?
7-deaza-2'-deoxyadenosine 5'-triphosphate + DNAn
diphosphate + ?
Substrates: -
Products: -
Products: -
?
8-oxo-dATP + DNAn
?
Substrates: dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2-deoxyribofuranosid-5-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
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8-oxo-dATP + DNAn
?
Substrates: dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2-deoxyribofuranosid-5-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme features poor filling activity of DNA gaps consisting of 15 bases, and exerts a more efficient action at the expense of DNA substrates containing a recessed end of equal length. Shortening the recessed end of DNA substrates decreases the rate of DNA elongation catalysed by ASFV Pol X. DNA binding is a step responsible for restraining the efficiency of ASFV Pol X catalytic action
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
African swine fever virus Badajoz 1971 Vero-adapted
Substrates: -
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
African swine fever virus Badajoz 1971 Vero-adapted
Substrates: the enzyme features poor filling activity of DNA gaps consisting of 15 bases, and exerts a more efficient action at the expense of DNA substrates containing a recessed end of equal length. Shortening the recessed end of DNA substrates decreases the rate of DNA elongation catalysed by ASFV Pol X. DNA binding is a step responsible for restraining the efficiency of ASFV Pol X catalytic action
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DnaG primase and DNA polymerase III holoenzyme are able to bind concurrently to a primed template during DNA replication
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: DNA replication can be accomplished using dNDPs as substrates. In thermophiles, genome replication may be less sensitive to the energy charge of the cell than in mesophiles because thermostable polymerases can accept the diphosphorylated as well as the triphosphorylated substrates. DNA replication is thus less affected by the intracellular ATP/ADP ratio, and the relatively high efficiency with which DNA is synthesized at elevated temperatures suggests that thermophiles may be able to dispense with the triphosphorylated substrates entirely
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: systematic study of competition PEX experiments with a series of 7-substituted 7-deazapurine and 5-substituted pyrimidine dNTPs bearing substituents of varying bulkiness in the presence of their natural counterparts (unmodified dNTPs). Most of these modified dNRTP's are good to excellent substrates for Bst and KOD XL polymerases and still moderate to good substrates for Pwo and Vent(exo-) polymerases. 7-Deazapurine dNTPs bearing p-electron-containing substituents (ethynyl and phenyl, as well as 7-vinyl-7-deazaadenine) are generally better substrates of Bst polymerase than natural dATP or dGTP, respectively. The corresponding 5-substituted cytosine dNTP's (dCRTP) are comparable to dCTP, whereas the 5-substituted uracil dURTPs are generally worse substrates than TTP. The measured kinetic parameters follow the same trend and confirm that 7-phenyl-7-deazapurine dNTPs have higher affinity to the active site of the polymerase than their natural counterparts
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the template-dependent polymerase that can repair non-complementary DNA double strand breaks with unpaired 3' primer termini by nonhomologous end joining. Its role is to fill short gaps arising as intermediates in the process of V(D)J recombination and during processing of accidental double strand breaks
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: Pol1 has flap endonuclease activity on the flap RNA strand of an RNA:DNA hybrid duplex as well as reverse transcriptase activity on a DNA-primed RNA template
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: Pol1 has flap endonuclease activity on the flap RNA strand of an RNA:DNA hybrid duplex as well as reverse transcriptase activity on a DNA-primed RNA template
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: DNA replication can be accomplished using dNDPs as substrates. In thermophiles, genome replication may be less sensitive to the energy charge of the cell than in mesophiles because thermostable polymerases can accept the diphosphorylated as well as the triphosphorylated substrates. DNA replication is thus less affected by the intracellular ATP/ADP ratio, and the relatively high efficiency with which DNA is synthesized at elevated temperatures suggests that thermophiles may be able to dispense with the triphosphorylated substrates entirely
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the yeast two-hybrid system is employed to define regions of intermolecular interaction between small subunit DP1, large subunit DP2, and proliferating cell nuclear antigen PCNA. Intra- and intermolecular interactions between these domains are verified by using surface plasmon resonance
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the yeast two-hybrid system is employed to define regions of intermolecular interaction between small subunit DP1, large subunit DP2, and proliferating cell nuclear antigen PCNA. Intra- and intermolecular interactions between these domains are verified by using surface plasmon resonance
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: systematic study of competition PEX experiments with a series of 7-substituted 7-deazapurine and 5-substituted pyrimidine dNTPs bearing substituents of varying bulkiness in the presence of their natural counterparts (unmodified dNTPs). Most of these modified dNRTP's are good to excellent substrates for Bst and KOD XL polymerases and still moderate to good substrates for Pwo and Vent(exo-) polymerases. 7-Deazapurine dNTPs bearing p-electron-containing substituents (ethynyl and phenyl, as well as 7-vinyl-7-deazaadenine) are generally better substrates of Bst polymerase than natural dATP or dGTP, respectively. The corresponding 5-substituted cytosine dNTPs (dCRTP) are comparable to dCTP, whereas the 5-substituted uracil dURTPs are generally worse substrates than TTP. The measured kinetic parameters follow the same trend and confirm that 7-phenyl-7-deazapurine dNTPs have higher affinity to the active site of the polymerase than their natural counterparts
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the complex DNA binding mechanism of a Y-family DNA polymerase involves aspects of both induced-fit and conformational selection mechanisms. Intradomain protein motions are observed throughout nucleotide binding and incorporation, some of which may kinetically limit the rate of correct nucleotide incorporation
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the complex DNA binding mechanism of a Y-family DNA polymerase involves aspects of both induced-fit and conformational selection mechanisms. Intradomain protein motions are observed throughout nucleotide binding and incorporation, some of which may kinetically limit the rate of correct nucleotide incorporation
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the catalytic core of yeast DNA polymerase eta prefers to incorporate dCTP opposite 7,8-dihydro-8-oxo-2'-deoxyguanosine (damage produced by reactive oxygen species in DNA). dCTP incorporation is slower than the dissociation of the polymerase from DNA. 57% of the extension products beyond the 7,8-dihydro-8-oxo-2'-deoxyguanosine are the products corresponding to the correct incorporation (C) and 43% corresponding to dATP misincorporation
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the catalytic core of yeast DNA polymerase eta prefers to incorporate dCTP opposite 7,8-dihydro-8-oxo-2'-deoxyguanosine (damage produced by reactive oxygen species in DNA). dCTP incorporation is slower than the dissociation of the polymerase from DNA. 57% of the extension products beyond the 7,8-dihydro-8-oxo-2'-deoxyguanosine are the products corresponding to the correct incorporation (C) and 43% corresponding to dATP misincorporation
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme is able to efficiently bypass uracil in DNA. The enzyme is halted by an AP site in DNA. Tga PolB extends the mismatched ends with reduced efficiencies. It possesses 3'-5' exonuclease activity. The enzyme can efficiently bind to ssDNA and primed DNA, and has a marked preference for primed DNA
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme is able to efficiently bypass uracil in DNA. The enzyme is halted by an AP site in DNA. Tga PolB extends the mismatched ends with reduced efficiencies. It possesses 3'-5' exonuclease activity. The enzyme can efficiently bind to ssDNA and primed DNA, and has a marked preference for primed DNA
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: systematic study of competition PEX experiments with a series of 7-substituted 7-deazapurine and 5-substituted pyrimidine dNTPs bearing substituents of varying bulkiness in the presence of their natural counterparts (unmodified dNTPs). Most of these modified dNRTP's are good to excellent substrates for Bst and KOD XL polymerases and still moderate to good substrates for Pwo and Vent(exo-) polymerases. 7-Deazapurine dNTPs bearing p-electron-containing substituents (ethynyl and phenyl, as well as 7-vinyl-7-deazaadenine) are generally better substrates of Bst polymerase than natural dATP or dGTP, respectively. The corresponding 5-substituted cytosine dNTPs (dCRTP) are comparable to dCTP, whereas the 5-substituted uracil dURTPs are generally worse substrates than TTP. The measured kinetic parameters follow the same trend and confirm that 7-phenyl-7-deazapurine dNTPs have higher affinity to the active site of the polymerase than their natural counterparts
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: DNA replication can be accomplished using dNDPs as substrates. In thermophiles, genome replication may be less sensitive to the energy charge of the cell than in mesophiles because thermostable polymerases can accept the diphosphorylated as well as the triphosphorylated substrates. DNA replication is thus less affected by the intracellular ATP/ADP ratio, and the relatively high efficiency with which DNA is synthesized at elevated temperatures suggests that thermophiles may be able to dispense with the triphosphorylated substrates entirely
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: systematic study of competition PEX experiments with a series of 7-substituted 7-deazapurine and 5-substituted pyrimidine dNTPs bearing substituents of varying bulkiness in the presence of their natural counterparts (unmodified dNTPs). Most of these modified dNRTP's are good to excellent substrates for Bst and KOD XL polymerases and still moderate to good substrates for Pwo and Vent(exo-) polymerases. 7-Deazapurine dNTPs bearing p-electron-containing substituents (ethynyl and phenyl, as well as 7-vinyl-7-deazaadenine) are generally better substrates of Bst polymerase than natural dATP or dGTP, respectively. The corresponding 5-substituted cytosine dNTPs (dCRTP) are comparable to dCTP, whereas the 5-substituted uracil dURTPs are generally worse substrates than TTP. The measured kinetic parameters follow the same trend and confirm that 7-phenyl-7-deazapurine dNTPs have higher affinity to the active site of the polymerase than their natural counterparts
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: DNA replication can be accomplished using dNDPs as substrates. In thermophiles, genome replication may be less sensitive to the energy charge of the cell than in mesophiles because thermostable polymerases can accept the diphosphorylated as well as the triphosphorylated substrates. DNA replication is thus less affected by the intracellular ATP/ADP ratio, and the relatively high efficiency with which DNA is synthesized at elevated temperatures suggests that thermophiles may be able to dispense with the triphosphorylated substrates entirely
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a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: activation energy analysis of the forward (DNA synthesis) and reverse (phosphorolysis of DNA) reactions catalyzed by the Taq DNA polymerase shows that DNA synthesis is strongly favored, allowing robust replication from low-energy substrates
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dATP + DNAn
?
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Substrates: Dbh is a distributive enzyme showing a low DNA and nucleotide binding affinity along with a slow polymerization rate. DNA binding occurs in a single step, diffusion-controlled manner. The rate-limiting step of nucleotide incorporation (correct and incorrect) is the chemical step (phosphoryl transfer) and not a conformational change of the enzyme. An induced fit mechanism to select and incorporate nucleotides during DNA polymerization can not be detected for the enzyme
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dATP + DNAn
?
Substrates: in addition to the correct insertion of dATP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
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dATP + DNAn
?
Substrates: -
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dATP + DNAn
?
Substrates: -
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dATP + DNAn
?
Substrates: in addition to the correct insertion of dATP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
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dATP + DNAn
?
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Substrates: activity with poly(dA) or poly(dT) as template, minimal primers are dAMP or dTMP. Lengthening of primers by each mononucleotide increases their affinity about 2.16-fold. The affinity of the primer d(pA)gp(rib*) with a deoxyribosylurea residue at the 3'-end does not differ essentially from that of d(pA)9. Substitution of the 3'-terminal nucleotide of a complementary primer for a noncomplementary nucleotide, e.g., substitution of 3'-terminal A for C in d(pA)10 in the reaction catalyzed on poly(dT), decreases the affinity of a primer by one order of magnitude
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dATP + DNAn
?
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Substrates: activity with poly(dA) or poly(dT) as template, minimal primers are dAMP or dTMP. Lengthening of primers by each mononucleotide increases their affinity about 2.16-fold. The affinity of the primer d(pA)gp(rib*) with a deoxyribosylurea residue at the 3'-end does not differ essentially from that of d(pA)9. Substitution of the 3'-terminal nucleotide of a complementary primer for a noncomplementary nucleotide, e.g., substitution of 3'-terminal A for C in d(pA)10 in the reaction catalyzed on poly(dT), decreases the affinity of a primer by one order of magnitude
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dATP + DNAn
diphosphate + DNAn+1
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Substrates: systematic determination of the single-turnover incorporation kinetics of all four native nucleotides and a set of Cy3-labeled nucleotides by the Klenow fragment of Escherichia coli DNA polymerase I
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dATP + DNAn
diphosphate + DNAn+1
-
Substrates: with labeled 20/33-mer primer-template duplex DNA
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dATP + DNAn
diphosphate + DNAn+1
-
Substrates: -
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dATP + DNAn
diphosphate + DNAn+1
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Substrates: with activated calf thymus DNA
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dATP + DNAn
diphosphate + DNAn+1
-
Substrates: dNTP insertion opposite a benzo[a]pyrene-N2-dG-adduct
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dCTP + DNAn
?
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Substrates: Dbh is a distributive enzyme showing a low DNA and nucleotide binding affinity along with a slow polymerization rate. DNA binding occurs in a single step, diffusion-controlled manner. The rate-limiting step of nucleotide incorporation (correct and incorrect) is the chemical step (phosphoryl transfer) and not a conformational change of the enzyme. An induced fit mechanism to select and incorporate nucleotides during DNA polymerization can not be detected for the enzyme
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dCTP + DNAn
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Substrates: in addition to the correct insertion of dCTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
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dCTP + DNAn
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Substrates: dTTP incorporation is the most preferred addition opposite the N6dA-(OH)2butyl-GSH adduct, N6dA-butanetriol adduct, or unmodified dA
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dCTP + DNAn
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Substrates: dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-methyl-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2-deoxyribofuranosid-5-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
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dCTP + DNAn
?
Substrates: -
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dCTP + DNAn
?
Substrates: -
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dCTP + DNAn
?
Substrates: in addition to the correct insertion of dCTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
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dCTP + DNAn
?
Substrates: dTTP incorporation is the most preferred addition opposite the N6dA-(OH)2butyl-GSH adduct, N6dA-butanetriol adduct, or unmodified dA
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dCTP + DNAn
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Substrates: dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-methyl-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2-deoxyribofuranosid-5-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
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dCTP + DNAn
diphosphate + DNAn+1
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Substrates: systematic determination of the single-turnover incorporation kinetics of all four native nucleotides and a set of Cy3-labeled nucleotides by the Klenow fragment of Escherichia coli DNA polymerase I
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dCTP + DNAn
diphosphate + DNAn+1
-
Substrates: -
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dCTP + DNAn
diphosphate + DNAn+1
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Substrates: with activated calf thymus DNA
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dCTP + DNAn
diphosphate + DNAn+1
-
Substrates: dNTP insertion opposite a benzo[a]pyrene-N2-dG-adduct
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deoxynucleoside triphosphate + DNAn
?
Substrates: the enzyme can preferentially insert C opposite N-(deoxyguanosin-8-yl)-2-acetylaminofluorene. An anti glycosidic torsion with C1'-exo deoxyribose conformation allows N-(deoxyguanosin-8-yl)-2-acetylaminofluorene to be WatsonCrick hydrogen-bonded with dCTP with modest polymerase perturbation, but other nucleotides are more distorting
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deoxynucleoside triphosphate + DNAn
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Substrates: the enzyme can preferentially insert C opposite N-(deoxyguanosin-8-yl)-2-acetylaminofluorene. An anti glycosidic torsion with C1'-exo deoxyribose conformation allows N-(deoxyguanosin-8-yl)-2-acetylaminofluorene to be WatsonCrick hydrogen-bonded with dCTP with modest polymerase perturbation, but other nucleotides are more distorting
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme can traverse a wide variety of DNA lesions. The enzyme is moderately processive. It can substitute for Taq in polymerase chain reaction (PCR) and can bypass DNA lesions that normally block Taq
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: specific preference for five base pairs, relatively low catalytic activity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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Substrates: natural substrate is gapped DNA
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: use of damaged DNA and dNTP substrates by the enzyme
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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Substrates: a fast fluorescence transition corresponding to conformational closing, and a slow fluorescence transition matching the rate of single-nucleotide incorporation. This transition represents a conformational event after chemistry, likely subdomain reopening
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the enzyme contains a double strand-dependent 3'-5' proofreading exonuclease activity, but lacks any 5'-3' exonuclease activity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: no exonuclease 5'--3' activity: pol II
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: can initiate polymer synthesis de novo, pol I
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time, cannot initiate a chain de novo, requires a primer which may be DNA or RNA
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: nicked duplex is no substrate of polymerase I
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: nicked duplex, as poly d(A-T), pol I
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: template specificity polymerase I, II and III
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: polymerase I plays a role in repair of chromosomal damage
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: physiological role of pol I and pol III
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: polymerase III is necessary for DNA replication
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: no exonuclease 5'--3' activity: pol II
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time, cannot initiate a chain de novo, requires a primer which may be DNA or RNA
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: nicked duplex, as poly d(A-T), pol I
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 3'--5' activity, pol epsilon
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: template specificity of DNA polymerase epsilon
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA substrate: gapped duplex or single-stranded 5'-ends smaller than 100 nucleotides, pol I, pol II and pol III
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: beta-polymerase can copy a synthetic ribohomopolymer such as (A)n*(dT)12 as well as the corresponding deoxyribohomopolymer (dA)n*(dT)12 or activated DNA, alpha-polymerase utilizes the deoxyribohomopolymer (dA)n*dT12-18 eight times better than (A)n*dT12
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: incorporates alpha-D-dNTPs and beta-D-dNTPs, L-dNTPs are no substrate
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: polymerase alpha: role in DNA replication
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: overview: physiological roles in replication and in DNA repair synthesis
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase gamma: required for mitochondrial DNA replication but encoded in the nucleus
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme exhibits its highest specific activity with gapped-duplex (activated) calf thymus DNA as the substrate, less activity with double-stranded salmon sperm DNA or heat-denatured double-stranded salmon sperm DNA
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 3'--5' activity
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: no detectable 3' exonuclease activity. CpDNApolI-dependent DNA synthesis is performed using DNA templates carrying different lesions. DNAs containing 2'-deoxyuridine (dU), 2'-deoxyinosine (dI) or 2'-deoxy-8-oxo-guanosine (8-oxo-dG) serve as templates as effectively as unmodified DNAs for CpDNApolI. Furthermore, the CpDNApolI can bypass natural apurinic/apyrimidinic sites (AP sites), deoxyribose (dR), and synthetic AP site tetrahydrofuran (THF). CpDNApolI can incorporate any dNMPs opposite both of deoxyribose and tetrahydrofuran with the preference to dAMP-residue. CpDNApolI preferentially extends primer with 3'-dAMP opposite deoxyribose during DNA synthesis, however all four primers with various 3'-end nucleosides (dA, dT, dC, and dG) opposite THF can be extended by CpDNApolI. Efficiently bypassing of AP sites by CpDNApolI is hypothetically attributed to lack of 3' exonuclease activity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: no detectable 3' exonuclease activity. CpDNApolI-dependent DNA synthesis is performed using DNA templates carrying different lesions. DNAs containing 2'-deoxyuridine (dU), 2'-deoxyinosine (dI) or 2'-deoxy-8-oxo-guanosine (8-oxo-dG) serve as templates as effectively as unmodified DNAs for CpDNApolI. Furthermore, the CpDNApolI can bypass natural apurinic/apyrimidinic sites (AP sites), deoxyribose (dR), and synthetic AP site tetrahydrofuran (THF). CpDNApolI can incorporate any dNMPs opposite both of deoxyribose and tetrahydrofuran with the preference to dAMP-residue. CpDNApolI preferentially extends primer with 3'-dAMP opposite deoxyribose during DNA synthesis, however all four primers with various 3'-end nucleosides (dA, dT, dC, and dG) opposite THF can be extended by CpDNApolI. Efficiently bypassing of AP sites by CpDNApolI is hypothetically attributed to lack of 3' exonuclease activity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: enzyme is active only in cells at meiotic prophase, in somatic cells it is in an inactive state
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the enzyme shows deoxynucleotide transferase activity, short patch DNA synthesis activity on heteropolymeric DNA substrate, 5'-deoxyribose phosphate lyase activity and base excision repair function in vitro
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Deinococcus radiodurans R1 / ATCC 13939 / DSM 20539
-
Substrates: the enzyme shows deoxynucleotide transferase activity, short patch DNA synthesis activity on heteropolymeric DNA substrate, 5'-deoxyribose phosphate lyase activity and base excision repair function in vitro
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA substrate: gapped duplex or single-stranded 5'-ends smaller than 100 nucleotides, pol I, pol II and pol III
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 3'--5' activity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: interaction of polymerases with template-primers containing chemically modified or damaged bases
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: fidelity of DNA replication
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase delta: with its auxiliary factor i.e. proliferating cell nuclear antigen, largely responsible for leading-strand synthesis
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: overview: physiological roles in replication and in DNA repair synthesis
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase gamma: required for mitochondrial DNA replication but encoded in the nucleus
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase alpha: with its associated primase largely responsible for lagging-strand synthesis
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: preference for poly(dA)/oligo(dT)10:1 as a template primer and has high processivity for DNA synthesis
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 3'--5' activity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: template specificity, enzyme overexpressed in E. coli
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 5'--3' activity
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 3'--5' activity, pol III
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: no exonuclease 5'--3' activity: pol II
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 3'--5' activity, pol II
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: can initiate polymer synthesis de novo, pol I
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: single strands, pol I, but not pol II and III
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: single-stranded 5'-ends greater than 100 nucleotides, pol I, but not pol II and pol III
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time, cannot initiate a chain de novo, requires a primer which may be DNA or RNA
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 3'--5' activity, pol I
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: template specificity of polymerase II
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: nicked duplex is no substrate of pol II and III of E. coli
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: nicked duplex, as poly d(A-T), pol I
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: can not initiate polymer synthesis de novo: pol II and III
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 5'--3' activity, pol I
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease activity associated with the replicative polymerase is contained within the epsilon subunit
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 3'--5' activity, pol I
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 3'--5' activity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease activity utilizes both, ssDNA and melted dsDNA templates, mismatched basepair is preferred over a correct basepair, removes an incorrect base incorporated opposite a template lesion
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: physiological role of pol I
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: physiological role of pol I, II and pol III
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: pol III can repair short gaps created by nuclease in duplex DNA, for efficient replication of the long, single-stranded templates pol III requires auxiliary subunits
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: polymerase III: role in replication of chromosomal DNA
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: polymerase II: role in DNA repair
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase V is involved in translesion synthesis and mutagenesis
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase V is involved in translesion synthesis and mutagenesis. Two factors are essential for efficient Pol V-mediated lesion bypass: 1. a DNA substrate onto which the beta-clamp is stably loaded and 2. an extended single-stranded RecA/ATP filament assembled downstream from the lesion site. For efficient bypass, Pol V needs to interact simultaneously with the beta-clamp and the 3' tip of the RecA filament
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: beta sliding clamp plays an essential role in pol V-dependent translesion DNA synthesis in vivo
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: a fast fluorescence transition corresponding to conformational closing, and a slow fluorescence transition matching the rate of single-nucleotide incorporation. This transition represents a conformational event after chemistry, likely subdomain reopening
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: wild-type DinB inserts deoxycytidine opposite N2-furfuryl-dG with 1015fold greater catalytic proficiency than opposite undamaged dG
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the Klenow fragment of DNA polymerase I is able to dimerize on a DNA primer/template. Dimerization is favored when the first molecule is bound in the polymerizing mode, but disfavored when it is bound in the editing mode. Self-association of the polymerase may play an important role in coordinating high-fidelity DNA replication
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
Products: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: bacteriohage T4 and bacteriophage RB69 replicative DNA polymerases exhibit differing abilities to form various base pairs. Formation of Watson-Crick base pairs occurs at similar rates between the two proteins but the incoming nucleotides are bound less tightly by RB69 DNA polymerase. Incorporation of an A opposite furan by T4 DNA polymerase is more rapid than for RB69 DNA polymerase with the two proteins having similar binding constants for the incoming dATP. An A:C mismatch is formed almost equally well by both proteins, while a significant difference exists when a T:T mismatch is formed
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: two proton transfers occur in the transition state for nucleotidyl-transfer reactions
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 3'--5' activity and 5'--3' activity, phage T7-induced DNA polymerase
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: nicked duplex is no substrate of phage T4-induced DNA polymerase
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time, cannot initiate a chain de novo, requires a primer which may be DNA or RNA
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: mechanical tension on DNA controls speed and direction of DNA polymerase motor
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the effects of varied DNA substrate size on the synthesis of DNA by the high fidelity T7 DNA polymerase: the T7 enzyme is highly sensitive in kinetic efficiency to size changes across this analog series. The T7 enzyme shows a strong dependence on substrate size and shows a preference for smaller substrates
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: gamma-phosphates of the incoming dNTP, contributing to charge neutralization and alignment of the alpha-phosphate for reaction
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA substrate: gapped duplex or single-stranded 5'-ends smaller than 100 nucleotides, pol I, pol II and pol III
Products: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: beta-polymerase can copy a synthetic ribohomopolymer such as (A)n*(dT)12 as well as the corresponding deoxyribohomopolymer (dA)n*(dT)12 or activated DNA, alpha-polymerase utilizes the deoxyribohomopolymer (dA)n*dT12-18 eight times better than (A)n*dT12
Products: -
Products: -
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
Products: -
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: overview: physiological roles in replication and in DNA repair synthesis
Products: -
Products: -
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase gamma: required for mitochondrial DNA replication but encoded in the nucleus
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: standard substrate PTJ1 and substrate PTJ2
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: standard substrate PTJ1 and substrate PTJ2
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: RNase H domain degrades RNA component of RNA-DNA hybrids
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Herpes simplex virus
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Herpes simplex virus
-
Substrates: beta-polymerase can copy a synthetic ribohomopolymer such as (A)n*(dT)12 as well as the corresponding deoxyribohomopolymer (dA)n*(dT)12 or activated DNA, alpha-polymerase utilizes the deoxyribohomopolymer (dA)n*dT12-18 eight times better than (A)n*dT12
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Herpes simplex virus
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA substrate: gapped duplex or single-stranded 5'-ends smaller than 100 nucleotides, pol I, pol II and pol III
Products: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: beta-polymerase can copy a synthetic ribohomopolymer such as (A)n*(dT)12 as well as the corresponding deoxyribohomopolymer (dA)n*(dT)12 or activated DNA, alpha-polymerase utilizes the deoxyribohomopolymer (dA)n*dT12-18 eight times better than (A)n*dT12
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: interaction of polymerases with template-primers containing chemically modified or damaged bases
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: fidelity of DNA replication
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: highly stereospecific, polymerase alpha, beta and epsilon incorporate only natural beta-D-dNTPs, L-dNTPs are no substrate
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: polymerase gamma also has proofreading activity with an RNA template, reverse transcriptase activity and incorporates ribonucleotide triphosphates into a DNA primer
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: overview: functional role of mammalian DNA polymerases
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: polymerase alpha: role in DNA replication
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: polymerase beta: role in DNA repair
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase delta: with its auxiliary factor i.e. proliferating cell nuclear antigen, largely responsible for leading-strand synthesis
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: overview: physiological roles in replication and in DNA repair synthesis
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase gamma: required for mitochondrial DNA replication but encoded in the nucleus
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase alpha: with its associated primase largely responsible for lagging-strand synthesis
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: Pol lambda plays a role in the short-patch base excision repair rather than contributes to the long-patch base excision repair pathway
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase mu possesses the ability to synthesize in vitro short fragments of DNA in the absence of a primer-template or even a primer or a template. Amino acid Phe506 of poly lambda is essential for the de novo synthesis
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: in addition to a slow and distributive DNA polymerase activity, Pol mu possesses a weak strand-displacement activity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: Pol eta effectively bypasses N2-methylguanine, N2-ethylguanine, N2-isobutylguanine, N2-benzylguanine, and N2-CH2(2-naphthyl)guanine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: Pol lambda is unable to catalyze strand displacement synthesis using nicked DNA, although this enzyme efficiently incorporates a dNMP into a one-nucleotide gap
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase lambda possesses the ability to synthesise in vitro short fragments of DNA in the absence of a primer-template or even a primer or a template. Amino acid Phe506 of poly lambda is essential for the de novo synthesis
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase iota may play a limited and error-prone role in translesion synthesis across the N2-guanine adducts (possibly medium sized adducts up to N2-benzylguanine) due to the low polymerization rates and high error rates
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: downstream strand and its 5'-phosphate moiety are critical to the polymerase efficiency of the enzyme. Nucleotide-gapped DNA substrates containing a 1,2-dideoxyribose-5-phosphate moiety (a 2-deoxyribose-5-phosphate mimic) moderately decrease the polymerase efficiency by 3.4fold
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: inefficient and error-prone bypass across bulky N2-guanine DNA adducts. Effectively bypasses N2-methylguanine and N2-ethylguanine, partially bypasses N2-isobutylguanine and N2-benzylguanine, and is blocked at N2-CH2(2-naphthyl)guanine, N2-CH2(9-anthracenyl)guanine, and N2-CH2(6-benzo[a]pyrenyl)guanine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: poly(dA)/oligo(dT)10:1. 2-thiomethyl-6-phenyl-4-(4'-hydroxybutyl)-1,2,4,-triazole (5,1-C)(1,2,4)triazine-7-one triphosphate can be incorporated on both templates but only by the Y505A mutant enzyme. N-(Benzyloxycarbonyl)-4-aminobutyl triphosphate can be incorporated by DNA pol lambda either wild type or the Y505A mutant, opposite to an abasic site only. Incorporation efficiency of (biphenylcarbonyl)-4-oxobutyl triphosphate by DNA polymmerase lambda wild type is 22fold higher opposite an abasic site than on the intact template. DNA polymerase lambda wild type incorporates (biphenylcarbonyl)-4-oxobutyl triphosphate 2.2fold more frequently than dCTP opposite the lesion. The DNA polymerase lambda Y505A mutant shows a 5.3fold preference for dCTP versus (biphenylcarbonyl)-4-oxobutyl triphosphate incorporation opposite the lesion
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: poly(dA)/oligo(dT)10:1. In the presence of Mn2+, DNA polymerase beta incorporates (biphenylcarbonyl)-4-oxobutyl triphosphate both on an intact template and opposite to an abasic site. DNA polymerase beta incorporates dCTP on the undamaged template, whereas it exclusively incorporates dATP opposite the abasic site. The incorporation efficiency of (biphenylcarbonyl)-4-oxobutyl triphosphate by DNA polymerase beta is 2fold higher in the presence of the undamaged template, with respect to the one carrying an abasic site. When Mn2+ is replaced by Mg2+, this difference becomes even more striking, so that (biphenylcarbonyl)-4-oxobutyl triphosphate can be exclusively incorporated on the undamaged in the presence of Mg2+, the incorporation of (biphenylcarbonyl)-4-oxobutyl triphosphate by DNA polymerase beta becomes strictly dependent on the presence of a templating base. Replacement of Mn2+ with Mg2+, however, greatly enhances the preference for incorporation of dCTP versus (biphenylcarbonyl)-4-oxobutyl triphosphate opposite a template G by DNA polymerase beta, which increases from 23fold to 239fold
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase mu could be involved in the repair of a DSB subset when resolution of junctions requires some gap filling
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: polymerase gamma is required for replication of mitochondrial DNA
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: DNA polymerase iota preferentially misincorporates nucleotides opposite thymines and halts replication at T bases
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: naturally occurring DNA structures are physiological substrates of both pol eta and pol kappa
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: with undamaged templating purines DNA polymerase iota normally favors Hoogsteen base pairing, DNA polymerase iota can incorporate nucleotides opposite a benzo[a]pyrene-derived adenine lesion
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: assays of Pol delta complexes on poly(dA)/oligo(dT) template/primers
Products: DNA products synthesized by Pol delta and its subassemblies on primed M13 DNA, overview
Products: DNA products synthesized by Pol delta and its subassemblies on primed M13 DNA, overview
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: reversibility of the polymerase reaction at the level of the template with diphosphate as leaving group, not with the alternative leaving groups, overview
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: herpes polymerase only elongates primase-synthesized primers at least 8 nucleotides long
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: role in DNA gap repair
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: two proton transfers in the transition state for nucleotidyl transfer
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA substrate: gapped duplex or single-stranded 5'-ends smaller than 100 nucleotides, pol I, pol II and pol III
Products: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: beta-polymerase can copy a synthetic ribohomopolymer such as (A)n*(dT)12 as well as the corresponding deoxyribohomopolymer (dA)n*(dT)12 or activated DNA, alpha-polymerase utilizes the deoxyribohomopolymer (dA)n*dT12-18 eight times better than (A)n*dT12
Products: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: overview: functional role of mammalian DNA polymerases
Products: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: overview: physiological roles in replication and in DNA repair synthesis
Products: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase gamma: required for mitochondrial DNA replication but encoded in the nucleus
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: template specificity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: standard substrate PTJ1 and substrate PTJ2
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: MacDinB-1 synthesizes long products (approximately 7.2 kb) in the presence of its cognate proliferating cell nuclear antigen (PCNA). MacDinB-1 works in an error-free mode to repair cyclobutane pyrimidine dimers
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 5'--3' activity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: no exonuclease 5'--3' activity: pol II
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: can initiate polymer synthesis de novo, pol I
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: single strands, pol I, but not pol II and III
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: single-stranded 5'-ends greater than 100 nucleotides, pol I, but not pol II and pol III
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time, cannot initiate a chain de novo, requires a primer which may be DNA or RNA
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 3'--5' activity, pol I
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 3'--5' activity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: nicked duplex is no substrate of polymerase I
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: nicked duplex, as poly d(A-T), pol I
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 5'--3' activity, pol I
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: beta-polymerase can copy a synthetic ribohomopolymer such as (A)n*(dT)12 as well as the corresponding deoxyribohomopolymer (dA)n*(dT)12 or activated DNA, alpha-polymerase utilizes the deoxyribohomopolymer (dA)n*dT12-18 eight times better than (A)n*dT12
Products: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the enzyme utilizes deaminated bases and is also able to amplify lambda DNA fragments using dUTP and dITP
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: beta-polymerase can copy a synthetic ribohomopolymer such as (A)n*(dT)12 as well as the corresponding deoxyribohomopolymer (dA)n*(dT)12 or activated DNA, alpha-polymerase utilizes the deoxyribohomopolymer (dA)n*dT12-18 eight times better than (A)n*dT12
Products: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: OsPOLP1 might be involved in a repair pathway similar to long-patch base excision repair. Possible role of POLPs in plastidial DNA replication and repair
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: OsPOLP1 efficiently catalyzed strand displacement on nicked DNA with a 5'-deoxyribose phosphate
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: polB and polD preferentially insert dAMP opposite an apurinic/apyrimidinic site, albeit inefficiently
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: PabPolD might play an important role in DNA replication likely together with PabpolB, suggesting that archaea require two DNA polymerases at the replication fork
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: both DNA polymerase D and DNA polymerases B are DNA polymerizing enzymes exclusively. DNA polymerase D has a preference for a primed template. DNA polymerase D is a primer-directed DNA polymerase independently of the primer composition whereas DNA polymerase B behaves as an exclusively DNA primer-directed DNA polymerase. Proliferating cell nuclear antigen is required for DNA polymerases D to perform efficient DNA synthesis but not DNA polymerases B. DNA polymerase D, but not DNA polymerase B, contains strand displacement activity. In the presence of PabPCNA, however, both DNA polymerases D and B show strand displacement activity. Direct interaction between DNA polymerase D and proliferating cell nuclear antigen is DNA-dependent
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: PCR performance and fidelity parameters are highest in the presence of 20 mM Tris-HCl, pH 9.0, 1.5 mM MgSO4, 25 mM KCl, 10 mM (NH4)2SO4 and 40 microM of each dNTP. Under these conditions, the error rate is 0.66.10(-6) mutations/nucleotide/duplication
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: PCR performance and fidelity parameters are highest in the presence of 20 mM Tris-HCl, pH 9.0, 1.5 mM MgSO4, 25 mM KCl, 10 mM (NH4)2SO4 and 40 microM of each dNTP. Under these conditions, the error rate is 0.66.10(-6) mutations/nucleotide/duplication
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: wild-type Pfu-Pol makes about one mistake for every 1000000 bases incorporated, wild-type variant Pfu-Pol(exo-)(D473F)is 60fold less accurate
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme has a template-primer preference which is characteristic of a replicative DNA polymerase
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Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: measurement of the incorporation of methyl-TTP into acid insoluble material. The single-stranded DNA substrate is more sensitive than the double stranded substrate. The polymerase and exonuclease domains in the family B DNA polymerases are functionally interdependent
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the DNA polymerase from Pyrococcus furiosus has the lowest error rate of any known polymerase in polymerase chain reaction amplification
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: replicative DNA polymerase
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme utilizes activated DNA as a template-primer, artificial substrate (activated poly(dA-dT)) is preferred by the enzyme. M13 single-stranded DNA primed with 17 base oligonucleotide is not a good substrate. DNA elongation ability of Pol II using a natural DNA template is much lower than that of Pol I from this organism and DNA synthesis of Pol II seems to be non-processive
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the enzyme plays an essential role in DNA replication, repair, and recombination
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the carboxyl-terminal (12551332) of the large subunit (DP2Pho) and two regions, the 201260 and 599622, of the small subunit (DP1Pho) are critical for the complex formation, and probable subunit interaction of PolDPho. The amino-terminal (1300) of DP2Pho is essential for the folding of PolDPho and is likely the oligomerization domain of PolDPho
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the functional motif, K253xRxxxD259 (outside known motifs Exo I, II, and III), that is important not only for exonuclease activity but also for polymerizing activity, confirms functional interdependence between the polymerase and exonuclease domains. The short loop region, K253G254R255, probably contributes to binding to DNA substrates
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: polymerase alpha: role in DNA replication
Products: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: a fast fluorescence transition corresponding to conformational closing, and a slow fluorescence transition matching the rate of single-nucleotide incorporation. This transition represents a conformational event after chemistry, likely subdomain reopening. Rotation of the Arg258 side chain is not rate-limiting in the overall kinetic pathway of Pol beta, yet is kinetically significant in subdomain reopening
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Ruellia sp.
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme can traverse a wide variety of DNA lesions. The enzyme is moderately processive. It can substitute for Taq in polymerase chain reaction (PCR) and can bypass DNA lesions that normally block Taq
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 3'--5' activity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: Sso DNA pol B1 recognizes the presence of uracil and hypoxanthine in the template strand and stalls synthesis 34 bases upstream of this lesion (read-ahead function). Sso DNA pol Y1 is able to synthesize across these and other lesions on the template strand. Sso DNA pol B1 physically interacts with DNA pol Y1. The region of DNA pol B1 responsible for this interaction has been mapped in the central portion of the polypeptide chain (from the amino acid residue 482 to 617)
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: with template guanine and Watson-Crick paired dCTP as the nascent base pair. Water-mediated and substrate-assisted mechanism: the initial proton transfer to the R-phosphate of the substrate via a bridging crystal water molecule is the rate-limiting step, the nucleotidyl-transfer step is associative with a metastable pentacovalent phosphorane intermediate, and the diphosphate leaving is facilitated by a highly coordinated proton relay mechanism through mediation of water which neutralizes the evolving negative charge. The conserved carboxylates, which retain their liganding to the two Mg2+ ions during the reaction process, are found to be essential in stabilizing transition states. This water-mediated and substrate-assisted mechanism takes specific advantage of the unique structural features of this low-fidelity lesion-bypass Y-family polymerase, which has a more spacious and solvent-exposed active site than replicative and repair polymerases
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: two representative types of lesions: (i) 7,8-dihydro-8-oxoguanine, a small, highly prevalent lesion caused by oxidative damage; and (ii) bulky lesions derived from the environmental pre-carcinogen benzo[a]pyrene. The diol epoxide (+)-(7R,8S,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[ a]pyrene reacts largely, but not exclusively, with the exocyclic amino group of guanine to produce the major 10S (+) trans-anti-BP-N2-dG adduct, that is bypassed by Dpo4
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: mechanism of purine-purine mispair formation, substrate specificity and binding structure, the kpol/Kd dNTP values for the insertion of dATP and dGTP opposite 7-deazaadenine and 7-deazaguanine are decreased over 10fold with respect to those of the unmodified nucleotides during formation of purine-purine mispairs. In addition, the rate of incorporation of 1-deaza-dATP opposite guanine is decreased 5fold. Dpo4 holds the incoming dNTP in the normal anti conformation while allowing the template nucleotide to change conformations to allow reaction to occur. This result may be functionally relevant in the replication of damaged DNA in that the polymerase may allow the template to adopt multiple configurations, overview
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: substrate is a 44-mer DNA template containing a site-specific cisplatin-d(GpG) adduct, Dpo4 is able to bypass a single, site-specifically placed cisplatin-d(GpG) adduct, although, the incorporation efficiency of dCTP opposite the first and second cross-linked guanine bases is decreased by 72 and 860fold, respectively, enzyme fidelity, overview
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the nucleotidyl-transfer reaction coupled with the conformational transitions in DNA polymerases is critical for maintaining the fidelity and efficiency of DNA synthesis, correct insertion of dCTP opposite 8-oxoguanine and quantum mechanics/molecular mechanics investigation of the chemical reaction in Dpo4 reveals water-dependent pathways and requirements for active site reorganization, overview
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: nucleotide selectivity opposite a benzo[a]pyrene-derived N2-dG adduct in DNA polymerase IV, 5'-slippage mechanism: the dATP can be inserted opposite the T on the 5' side of the adduct G1*, in which the unadducted G2, rather than G1*, is skipped, to produce a -1 deletion, molecular modeling and dynamics simulations, overview
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: two representative types of lesions: (i) 7,8-dihydro-8-oxoguanine, a small, highly prevalent lesion caused by oxidative damage; and (ii) bulky lesions derived from the environmental pre-carcinogen benzo[a]pyrene, Dpo4 bypasses 8-oxoG accurately
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: DNA polymerase IV (Dpo4) shows 90-fold higher incorporation efficiency of dCTP > dATP opposite 8-oxoG and 4-fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. Extension beyond an 8-oxoG:C pair is similar to G:C and faster than for an 8-oxoG:A pair, in contrast to other polymerases. dCTP insertion opposite 8-oxoG was lower than for opposite guanine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: products of replication of polycyclic aromatic hydrocarbon-modified DNA by the translesion DNA polymerase Dpo4 are complex
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: modeling and molecular dynamics simulations for 2'-deoxy-8-[(1-methyl-6-phenyl-1H-imidazo[4,5-b]pyridin-2-yl)amino]guanosine suggest that the adduct would increase the infidelity of Dpo4 and hinder translocation by the enzyme
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the rate-constant defining Dpo4-catalyzed incorporation of dCTP is about 6-fold slower for incorporation opposite O6-MeG relative to G. The basis for the decreased rate is revealed by the crystal structure to be formation of a wobble base pairing between O6-MeG and C
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme shows a limited decrease in catalytic efficiency (kcat/Km) for insertion of dCTP opposite a series of N2-alkylguanine templates of increasing size from (methyl (Me) to (9-anthracenyl)-Me (Anth)). Fidelity is maintained with increasing size up to (2-naphthyl)-Me (Naph). The catalytic efficiency increases slightly going from the N2-NaphG to the N2-AnthG substrate, at the cost of fidelity. A set of oligonucleotides differing only in their N2-substitution at a single G site is used in this study with Dpo4
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the pre-steady-state kinetic methods is used to determine the base substitution fidelity and mismatch extension fidelity of PolB1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: propenal and malondialdehyde react with DNA to form adducts, including 3-(2'-deoxy-beta-D-erythro-pentofuranosyl) pyrimido[1,2-alpha]purin-10(3H)-one (M1dG). When paired opposite cytosine in duplex DNA at physiological pH, M1dG undergoes ring opening to form N2-(3-oxo-1-propenyl)-dG. To improve the understanding of the basis for M1dG-induced mutagenesis, the mechanism of translesion DNA synthesis opposite M1dG by the model Y-family polymerase Dpo4 is studied at a molecular level using kinetic and structural approaches. The enzyme can bypass the exocyclic M1dG adduct in largely an error-prone fashion
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: approximately 2/3 of the errors made by the enzyme are single-base substitutions, of which 58% are C->T transition. Frameshift mutations, mostly resulting from single-base deletions, account for 19% of the total errors. An exonuclease-deficient mutant of Sso pol B1 is three times as mutagenic as the wild-type enzyme, suggesting that the intrinsic proofreading function contributed only modestly to the fidelity of the enzyme
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: translesion synthesis of the 7-(2-oxoheptyl)-1,N2-etheno-2'-deoxyguanosine lesion by the enzyme in 5'-TXG-3' and 5'-CXG-3' local sequence contexts is examined and compared to 1,N2-etheno-2'-deoxyguanosine lesions
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme bypasses aflatoxin B1-N7-dG in an error-free manner but conducts error-prone replication past the aflatoxin B1-formamidopyrimidine adduct, including misinsertion of dATP
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: replication bypass studies in vitro reveal that the polymerase inserts dNTPs opposite the (6S,8R,11S)-trans-4-hydroxynonenal-1,N2-dGuo adduct in a sequence-specific manner. If the template 5'-neighbor base is dCyt, the polymerase inserts primarily dGTP. If the template 5'-neighbor base is dThy, the polymerase inserts primarily dATP
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme is nonprocessive and can bypass an abasic site
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: in the absence of additional cofactor the enzyme is an essentially distributive enzyme that only extends primers by 1-2 nt per binding event. At high enzyme to primer/template ratios, dissociation and rebinding of the enzyme to the primer/template is robust and can lead to the synthesis of polynucleotide chains of several hundred nucleotides in length
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: ribonucleotide discrimination by the DinB homolog (Dbh) DNA polymerase is as stringent as in other polymerases. When making a deletion error, ribonucleotide discrimination by wild-type and F12A Dbh is the same as in normal DNA synthesis
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: bypass of apurinic/apyrimidinic sites lacking A or G is nearly 100% mutagenic. The majority (7080%) of bypass events are insertion of dAMP opposite the apurinic/apyrimidinic site
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme can efficiently incorporate nucleotides opposite 8-oxoG and extend from an 8-oxoG:C base pair with a mechanism similar to that observed for the replication of undamaged DNA
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the enzyme bypasses DNA adducts pyrrolo-deoxycytosine, dP, N6-furfuryl-deoxyadenosine, and 1,N6-ethenodeoxyadenosine in a process known as translesion synthesis
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis 2-OH-dATP is predominantly incorporated opposite guanine and thymine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis. 2-OH-dATP is predominantly incorporated opposite guanine and thymine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: deamination of cytosine to uracil is a hydrolytic reaction that is greatly accelerated at high temperatures. The resulting uracil pairs with adenine during DNA replication, thereby inducing G:C to A:T transitions in the progeny. B-family DNA polymerases from hyperthermophilic archaea recognize the presence of uracil in DNA and stall DNA synthesis. Although PolB1 per se specifically binds to uracil-containing single-stranded DNA, the binding efficiency is substantially enhanced by the initiation of DNA synthesis. The generation of ds DNA is significantly inhibited, however, by the presence of template uracil. Pol B1 more efficiently recognizes uracil in DNA during DNA synthesis rather than during random diffusion in solution. Single molecules of Pol B1 bind to template uracil and stall DNA synthesis
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the enzyme incorporates dTTP in a 61 mer template containing pyrrolo-deoxycytosine, dP, N6-furfuryl-deoxyadenosine, and 1,N6-ethenodeoxyadenosine (translesion synthesis)
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by the enzyme, with hydrogen bonding capacity being a major influence. Modifications at the C2-position of dCTP increases the selectivity for incorporation opposite O6-methylguanine without a significant loss of efficiency
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the enzyme binds to DNA in at least three distinct conformations. The relative frequency of each conformation can be modulated by both the identity of the primer 3' terminus and the presence of an incoming dNTP
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: low fidelity. When copying undamaged DNA, Dpo4 is highly inaccurate for essentially all types of single base substitutions and deletions in a large number of different sequence contexts
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme is inefficient at extending mispairs opposite a template G or T, which include, a G*T mispair expected to conform closely to Watson-Crick geometry. It is hindered in extending a G*T mismatch by a reverse wobble
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: even at 60°C, excessive amounts of Dpo4 are needed to carry out minimal bypass of the cyclobutane pyrimidine dimers
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase pol Y1 exclusively incorporates 8-OH-GTP opposite adenine. DNA polymerase pol Y1 incorporates 2-OH-dATP predominantly opposite guanine and thymine. DNA polymerase pol B1 incorporates 8-OH-GTP opposite adenine and cytosine. DNA polymerase pol B1 incorporates 2-OH-dATP opposite thymine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exclusively incorporates 8-OH-GTP opposite adenine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: when insertion is opposite an unmodified G, insertion of dATP or dGTP is 1000 less efficient than dCTP. For insertion opposite 8-oxoG, the order of decreasing efficiency is dCTP, dATP, dGTP, with an order of magnitude or more difference in catalytic efficiency (kcat/Km) in each pair of comparisons. The insertion of dCTP opposite G and 8-oxoG shows similar catalytic efficiency, even with differences in the trends for kcat and Km. 90fold higher incorporation efficiency of dCTP compared to dATP opposite 8-oxoG and 4fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. The 8-oxoG:C pair shows classic Watson-Crick geometry; the 8-oxoG:A pair is in the syn:anti configuration, with the A hybridized in a Hoogsteen pair with 8-oxoG. With dGTP placed opposite 8-oxoG, pairing was not to the 8-oxoG but to the 5'C (and in classic Watson-Crick geometry), consistent with the low frequency of this frameshiftevent observed in the catalytic assays
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme shows little decreases opposite N2-MeG, 13fold decrease opposite N2-BzG but 260-370fold decreases opposite O6-MeG, O6-BzG, and the abasic site site as compared to G. Dpo4 favored correct C insertion opposite opposite N2-MeG, opposite O6-MeG, opposite an abasic site site and oppositeN2-BzG. DNA polymerase Vent (exo-) from Thermococcus litoralis is as or more efficient as polymerase Dpo4 from Sulfolobus solfataricus in synthesis opposite O6-MeG and AP lesions, whereas DNA polymerase Dpo4 from Sulfolobus solfataricus is much or more efficient opposite N2-alkylGs than DNA polymerase Vent (exo-) from Thermococcus litoralis, irrespective of DNA-binding affinity. DNA polymerase Dpo4 strongly favors minor-groove N2-alkylG lesions over major-groove or noninstructive lesions
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: DNA polymerase Dpo4 can replicate past a variety of DNA lesions. When replicating undamaged DNA, the enzyme is prone to make base pair substitutions
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: mechanism of template-independent nucleotide incorporation. Based on the efficiency ratios, Dpo4 selects nucleotides for blunt-end addition in the order of decreasing efficiency: dATP, dTTP, dCTP, dGTP, with dATP favored by five to 50fold over the other nucleotides. The first bluntend dATP incorporation is 80fold more efficient than the second, and among natural deoxynucleotides, dATP is the preferred substrate due to its stronger intrahelical base-stacking ability
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: while showing efficient bypass, the enzyme pauses when incorporating nucleotides directly opposite and one position downstream from an abasic lesion because of a drop of several orders of magnitude in catalytic efficiency. Biphasic kinetics for incorporation indicating that Dpo4 primarily forms a nonproductive complex with DNA that converts slowly to a productive complex. These strong pause sites are mutational hot spots with the embedded lesion even affecting the efficiency of five to six downstream incorporations
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme is able to bypass N-(deoxyguanosin-8-yl)-1-aminopyrene, but pauses strongly at two sites: opposite the lesion and immediately downstream from the lesion. Both nucleotide incorporation efficiency and fidelity decrease significantly at the pause sites, especially during extension of the bypass product. Interestingly, a 4-fold tighter inding affinity of damaged DNA to Dpo4 DNA polymerase promotes catalysis through putative interactions between the active site residues of Dpo4 and 1-aminopyrene moiety at the first pause site
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the molecular dynamics simulations suggest that mismatched nucleotide insertion opposite 10S-(+)-trans-anti-[benzo[a]pyrene]-N2-dG is increased at 55°C compared with 37°C because the higher temperature shifts the preference of the damaged base from the anti to the syn conformation, with the carcinogen on the more open major groove side. The mismatched dNTP structures are less distorted when the damaged base is syn than when it is anti, at the higher temperature. With the normal partner dCTP, the anti conformation with close to Watson-Crick alignment remains more favorable. The molecular dynamics simulations are consistent with the kcat values for nucleotide incorporation opposite the lesion studied, providing structural interpretation of the experimental observations. The observed temperature effect suggests that conformational flexibility plays a role in nucleotide incorporation and bypass fidelity opposite 10S-(+)-trans-anti-[benzo[a]pyrene]-N2-dG by Dpo4
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: GTP incorporation by the wild-type enzyme is about 1000fold slower than dGTP incorporation. The rate of GTP incorporation by the mutant enzyme F12A Dbh is 2-3fold slower than incorporation of dGTP. The enzyme makes single-base deletion errors at high frequency in particular sequence contexts
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: ATP binding to replication factor C is sufficient for loading the heterotrimeric PCNA123 [proliferating cell nuclear antigen (PCNA)] clamp onto DNA that includes a rate-limiting conformational rearrangement of the complex. ATP hydrolysis is required for favorable recruitment and interactions with the replication polymerase (PolB1) that most likely include clamp closing and dissociation of replication factor C. Surprisingly, the assembled holoenzyme complex synthesizes DNA distributively and with low processivity, unlike most other well-characterized DNA polymerase holoenzyme complexes. PolB1 repeatedly disengages from the DNA template, leaving PCNA123 behind. Interactions with a C-terminal PCNA-interacting peptide (PIP) motif on PolB1 specifically with PCNA2 are required for holoenzyme formation and continuous re-recruitment during synthesis
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the enzyme catalyze DNA synthesis using either activated calf thymus DNA or oligonucleotide-primed single-stranded DNA as a template
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the conformational dynamics of the Y-family DNA polymerase Dpo4 on DNA is characterized in real time using single-molecule Förster resonance energy transfers (mFRET). Two different binary complexes consistent with DNA translocation in the polymerase active site
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: distributive enzyme but a substantial increase in the processivity was observed on poly(dA)-oligo(dT) in the presence of proliferating cell nuclear antigen (039p or 048p) and replication factor CRFC. The length of the synthesized DNA product reaches at least 200 nucleotides
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the enzyme possess a remarkable DNA stabilizing ability for maintaining weak base pairing interactions to facilitate primer extension. This thermal stabilization by Dpo1 allows for template-directed synthesis at temperatures more than 30°C above the melting temperature of naked DNA. Dpo1 elongates single stranded DNA in template-dependent and template-independent manners. Initial deoxyribonucleotide incorporation is complementary to the template. Rate-limiting steps that include looping back and annealing to the template allow for a unique template-dependent terminal transferase activity. Dpo1 also displays a competing terminal deoxynucleotide transferase activity unlike any other B-family DNA polymerase
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: an abasic lesion causes Dpo4 to switch from a normal to a very mutagenic mode of replication. Incorporation upstream of the abasic lesion is replicated error-free. Once Dpo4 encounters the lesion, synthesis became sloppy, with bypass products containing a myriad of mutagenic events. Incorporation of dAMP (29%) and dCMP (53%) opposite the abasic lesion at 37°C correlates exceptionally well with our kinetic results and demonstrates two dominant bypass pathways via the A-rule and the lesion loop-out mechanism. The percentage of overall frameshift mutations increases from 71% (37°C) to 87% (75°C)
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme bypasses Pt-GG DNA (1,2-intrastrand covalent linkage, cis-Pt-1,2-d(GpG)). This is a dynamic process, in which the lesion is converted from an open and angular conformation at the first insertion to a depressed and nearly parallel conformation at the subsequent reaction stages to fit into the active site of Dpo4
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: Dpo4 predominantly uses a template slippage deletion mechanism when replicating repetitive DNA sequences. Dpo4 stabilizes the skipped template base in an extrahelical conformation between the polymerase and the little-finger domains of the enzyme
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the fidelity of Dpo4 is in the range of 0.001-0.0001. The ground-state binding affinity of correct nucleotides is 10-50-fold weaker than those of replicative DNA polymerases. The affinity of incorrect nucleotides for Dpo4 is about 2-10-fold weaker than that of correct nucleotides. The mismatched dCTP has an affinity similar to that of the matched nucleotides when it is incorporated against a pyrimidine template base flanked by a 5'-template guanine. The mismatch incorporation rates, regardless of the 5'-template base, are about 2-3 orders of magnitude slower than the incorporation rates for matched nucleotides, which is the predominant contribution to the fidelity of Dpo4
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme does not efficiently insert nucleotides opposite to the (6S,8R,11S)-1,N2-deoxyguanosine adduct, consistent with the low levels of Gua->Thy mutations. However it extends past the (6S,8R,11S)-1,N2-deoxyguanosine:dCyd pair. A series of ternary (Dpo4-DNA-dNTP) structures with (6S,8R,11S)-1,N2-deoxyguanosine-adducted templates suggest that during replication, the ring-closed (6S,8R,11S)-1,N2-deoxyguanosine lesion at the active site hinders incorporation of dNTPs opposite the lesion, whereas the ring-opened form of the lesion in the (6S,8R,11S)-1,N2-deoxyguanosine:dCyd pair allows for extension to full-length product
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: proliferating cell nuclear antigen facilitates DNA synthesis with Dpo3, as with Dpo1 and Dpo4, but very weakly with Dpo2. DNA synthesis in the presence of proliferating cell nuclear antigen, replication factor C, and single-stranded binding protein is most processive with DNA polymerase Dpo1 in comparison to DNA polymerase Dpo3 and Dpo4. DNA lesion bypass DNA synthesis in the presence of proliferating cell nuclear antigen, replication factor C, and single-stranded binding protein is most effective with DNA polymerase Dpo4 in comparison to DNA polymerase Dpo1 and Dpo3. Both Dpo2 and Dpo3, but not Dpo1, bypass hypoxanthine and 8-oxoguanine. Dpo2 and Dpo3 bypass uracil and cis-syn cyclobutane thymine dimer, respectively. DNA polymerase Dpo2 and Dpo3 possess very low DNA polymerase and 3' to 5' exonuclease activities in vitro compared with Dpo1 and Dpo4
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: in addition to the correct insertion of dCTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: dTTP incorporation is the most preferred addition opposite the N6dA-(OH)2butyl-GSH adduct, N6dA-butanetriol adduct, or unmodified dA
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: Dbh polymerase is much less accurate than the classical polymerases, but it shows a remarkable tendency to skip over a template pyrimidine positioned immediately 3' to a G residue, generating a single-base deletion. The rate of incorporation of dCTP opposite a template G is about 10fold faster than for the other three dNTPs opposite their complementary partners
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the rate of mismatched nucleotide incorporation is greater than the rate of correct dC insertion at 55 °C, whereas at 37 °C there is little selectivity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: incorporated of 2-amino-3-methylimidazo[4,5-f]quinoline C8- and N2-dGuo adducts into the G1- and G3-positions of the NarI recognition sequence (5'-G1G2CG3CC-3'), which is a hotspot for arylamine modification. Replication of the C8-adduct at the G3-position results in two-base deletion, whereas error-free bypass and extension is observed at the G1-position. The N2-adduct is bypassed and extended when positioned at the G1-position, and the error-free product is observed. The N2-adduct at the G3-position is more blocking and is bypassed and extended only by Dpo4 to produce an errorfree product. The replication of the 2-amino-3-methylimidazo[4,5-f]quinoline-adducts of dGuo is strongly influenced by the local sequence and the regioisomer of the adduct
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: an abasic lesion causes the enzyme to switch from a normal to a very mutagenic mode of replication
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the initial enzyme/DNA/dNTP complex undergoes a rapid (18/s), reversible (21/s) conformational change, followed by relatively rapid phosphodiester bond formation (11/s) and then fast release of pyrophosphate, followed by a rate-limiting relaxation of the active conformation (2/s) and then rapid DNA release, yielding an overall steady-state kcat of less than 1/s
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: removal of the 2-amino group from the template dG (i.e. deoxyinosine) has little impact on the catalytic efficiency of either polymerase, although the misincorporation frequency is increased by an order of magnitude. Deoxyxanthosine is highly miscoding with both polymerases, and incorporation of several bases is observed. The addition of bromine or oxygen at C2 lowers the Tm further, strongly inhibits and increases the frequency of misincorporation
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the binding of a correct nucleotide induces a fast and surprising DNA translocation event. All four domains of the polymerase rapidly move in a synchronized manner before and after the polymerization reaction. Repositioning of active site residues is the rate-limiting step during correct nucleotide incorporation. The motions of the polymerase and the polymerase bound DNA substrate are tightly coupled to catalysis
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: Dpo4 in most cases selects the correctly paired partner for each benzo-expanded DNA base, but with efficiency lowered by the enlarged pair size
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the rate of insertion of dNTPs opposite and extension past both O2-[4-(3-pyridyl)-4-oxobut-1-yl]-thymidine and O2-methylthymidine is measured. The size of the alkyl chain only marginally affects the reactivity and the specificity of adduct bypass is very low. Dpo4 catalyzes the incorporation opposite and extension past the adducts approximately 1000fold more slowly than undamaged DNA. dA is the preferred base pair partner for O2-[4-(3-pyridyl)-4-oxobut-1-yl]-thymidine and dT is the preferred base pair partner for O2-methylthymidine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: relative to undamaged DNA the enzyme generates far more mutations (base deletions, insertions, and substitutions) with a DNA template containing a site-specifically placed N-(deoxyguanosin-8-yl)-1-aminopyrene. Opposite N-(deoxyguanosin-8-yl)-1-aminopyrened and at an immediate downstream template position, the most frequent base substitutions are dA
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: ring-opening of the 3-(2'-deoxy-beta-D-erythro-pentofuranosyl)-5,6,7,8-tetrahydro-8-hydroxypyrimido[1,2-a] purin-10(3H)-one adduct promotes error-free bypass by the Sulfolobus solfataricus DNA polymerase Dpo4
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: bifunctional enzyme EC 2.7.7.7/EC 3.1.11.2. The polymerization and the 3'-5' exonuclease activity of a family B DNA polymerase can be ascribed to physically distinct modules of the enzyme molecule
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme inefficiently bypasses (5'S)-8,5'-cyclo-2'-deoxyguanosine with dCTP preferably incorporated and dATP misincorporated. (5'S)-8,5'-cyclo-2'-Deoxyguanosine attenuates K(d,dNTP,app) and k(pol)
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme inefficiently bypasses (5'S)-8,5'-cyclo-2'-deoxyguanosine with dCTP preferably incorporated and dTTP misincorporated. The (5'S)-8,5'-cyclo-2'-Deoxyguanosine-adduct-duplex complex causes 6fold decrease in Dpo4:DNA binding affinity, and significantly reduces the concentration of the productive Dpo4:DNA:dCTP complex
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 3'--5' activity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis 2-OH-dATP is predominantly incorporated opposite guanine and thymine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis. 2-OH-dATP is predominantly incorporated opposite guanine and thymine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase pol Y1 exclusively incorporates 8-OH-GTP opposite adenine. DNA polymerase pol Y1 incorporates 2-OH-dATP predominantly opposite guanine and thymine. DNA polymerase pol B1 incorporates 8-OH-GTP opposite adenine and cytosine. DNA polymerase pol B1 incorporates 2-OH-dATP opposite thymine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exclusively incorporates 8-OH-GTP opposite adenine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: DNA polymerase IV (Dpo4) shows 90-fold higher incorporation efficiency of dCTP > dATP opposite 8-oxoG and 4-fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. Extension beyond an 8-oxoG:C pair is similar to G:C and faster than for an 8-oxoG:A pair, in contrast to other polymerases. dCTP insertion opposite 8-oxoG was lower than for opposite guanine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: when insertion is opposite an unmodified G, insertion of dATP or dGTP is 1000 less efficient than dCTP. For insertion opposite 8-oxoG, the order of decreasing efficiency is dCTP, dATP, dGTP, with an order of magnitude or more difference in catalytic efficiency (kcat/Km) in each pair of comparisons. The insertion of dCTP opposite G and 8-oxoG shows similar catalytic efficiency, even with differences in the trends for kcat and Km. 90fold higher incorporation efficiency of dCTP compared to dATP opposite 8-oxoG and 4fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. The 8-oxoG:C pair shows classic Watson-Crick geometry; the 8-oxoG:A pair is in the syn:anti configuration, with the A hybridized in a Hoogsteen pair with 8-oxoG. With dGTP placed opposite 8-oxoG, pairing was not to the 8-oxoG but to the 5'C (and in classic Watson-Crick geometry), consistent with the low frequency of this frameshiftevent observed in the catalytic assays
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: products of replication of polycyclic aromatic hydrocarbon-modified DNA by the translesion DNA polymerase Dpo4 are complex
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: modeling and molecular dynamics simulations for 2'-deoxy-8-[(1-methyl-6-phenyl-1H-imidazo[4,5-b]pyridin-2-yl)amino]guanosine suggest that the adduct would increase the infidelity of Dpo4 and hinder translocation by the enzyme
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the rate-constant defining Dpo4-catalyzed incorporation of dCTP is about 6-fold slower for incorporation opposite O6-MeG relative to G. The basis for the decreased rate is revealed by the crystal structure to be formation of a wobble base pairing between O6-MeG and C
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme shows a limited decrease in catalytic efficiency (kcat/Km) for insertion of dCTP opposite a series of N2-alkylguanine templates of increasing size from (methyl (Me) to (9-anthracenyl)-Me (Anth)). Fidelity is maintained with increasing size up to (2-naphthyl)-Me (Naph). The catalytic efficiency increases slightly going from the N2-NaphG to the N2-AnthG substrate, at the cost of fidelity. A set of oligonucleotides differing only in their N2-substitution at a single G site is used in this study with Dpo4
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the pre-steady-state kinetic methods is used to determine the base substitution fidelity and mismatch extension fidelity of PolB1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: translesion synthesis of the 7-(2-oxoheptyl)-1,N2-etheno-2'-deoxyguanosine lesion by the enzyme in 5'-TXG-3' and 5'-CXG-3' local sequence contexts is examined and compared to 1,N2-etheno-2'-deoxyguanosine lesions
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme bypasses aflatoxin B1-N7-dG in an error-free manner but conducts error-prone replication past the aflatoxin B1-formamidopyrimidine adduct, including misinsertion of dATP
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: in the absence of additional cofactor the enzyme is an essentially distributive enzyme that only extends primers by 1-2 nt per binding event. At high enzyme to primer/template ratios, dissociation and rebinding of the enzyme to the primer/template is robust and can lead to the synthesis of polynucleotide chains of several hundred nucleotides in length
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme can efficiently incorporate nucleotides opposite 8-oxoG and extend from an 8-oxoG:C base pair with a mechanism similar to that observed for the replication of undamaged DNA
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: low fidelity. When copying undamaged DNA, Dpo4 is highly inaccurate for essentially all types of single base substitutions and deletions in a large number of different sequence contexts
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme is inefficient at extending mispairs opposite a template G or T, which include, a G*T mispair expected to conform closely to Watson-Crick geometry. It is hindered in extending a G*T mismatch by a reverse wobble
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: even at 60°C, excessive amounts of Dpo4 are needed to carry out minimal bypass of the cyclobutane pyrimidine dimers
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis 2-OH-dATP is predominantly incorporated opposite guanine and thymine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis. 2-OH-dATP is predominantly incorporated opposite guanine and thymine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase pol Y1 exclusively incorporates 8-OH-GTP opposite adenine. DNA polymerase pol Y1 incorporates 2-OH-dATP predominantly opposite guanine and thymine. DNA polymerase pol B1 incorporates 8-OH-GTP opposite adenine and cytosine. DNA polymerase pol B1 incorporates 2-OH-dATP opposite thymine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exclusively incorporates 8-OH-GTP opposite adenine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme shows little decreases opposite N2-MeG, 13fold decrease opposite N2-BzG but 260-370fold decreases opposite O6-MeG, O6-BzG, and the abasic site site as compared to G. Dpo4 favored correct C insertion opposite opposite N2-MeG, opposite O6-MeG, opposite an abasic site site and oppositeN2-BzG. DNA polymerase Vent (exo-) from Thermococcus litoralis is as or more efficient as polymerase Dpo4 from Sulfolobus solfataricus in synthesis opposite O6-MeG and AP lesions, whereas DNA polymerase Dpo4 from Sulfolobus solfataricus is much or more efficient opposite N2-alkylGs than DNA polymerase Vent (exo-) from Thermococcus litoralis, irrespective of DNA-binding affinity. DNA polymerase Dpo4 strongly favors minor-groove N2-alkylG lesions over major-groove or noninstructive lesions
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: DNA polymerase Dpo4 can replicate past a variety of DNA lesions. When replicating undamaged DNA, the enzyme is prone to make base pair substitutions
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: mechanism of template-independent nucleotide incorporation. Based on the efficiency ratios, Dpo4 selects nucleotides for blunt-end addition in the order of decreasing efficiency: dATP, dTTP, dCTP, dGTP, with dATP favored by five to 50fold over the other nucleotides. The first bluntend dATP incorporation is 80fold more efficient than the second, and among natural deoxynucleotides, dATP is the preferred substrate due to its stronger intrahelical base-stacking ability
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: while showing efficient bypass, the enzyme pauses when incorporating nucleotides directly opposite and one position downstream from an abasic lesion because of a drop of several orders of magnitude in catalytic efficiency. Biphasic kinetics for incorporation indicating that Dpo4 primarily forms a nonproductive complex with DNA that converts slowly to a productive complex. These strong pause sites are mutational hot spots with the embedded lesion even affecting the efficiency of five to six downstream incorporations
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme is able to bypass N-(deoxyguanosin-8-yl)-1-aminopyrene, but pauses strongly at two sites: opposite the lesion and immediately downstream from the lesion. Both nucleotide incorporation efficiency and fidelity decrease significantly at the pause sites, especially during extension of the bypass product. Interestingly, a 4-fold tighter inding affinity of damaged DNA to Dpo4 DNA polymerase promotes catalysis through putative interactions between the active site residues of Dpo4 and 1-aminopyrene moiety at the first pause site
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the molecular dynamics simulations suggest that mismatched nucleotide insertion opposite 10S-(+)-trans-anti-[benzo[a]pyrene]-N2-dG is increased at 55°C compared with 37°C because the higher temperature shifts the preference of the damaged base from the anti to the syn conformation, with the carcinogen on the more open major groove side. The mismatched dNTP structures are less distorted when the damaged base is syn than when it is anti, at the higher temperature. With the normal partner dCTP, the anti conformation with close to Watson-Crick alignment remains more favorable. The molecular dynamics simulations are consistent with the kcat values for nucleotide incorporation opposite the lesion studied, providing structural interpretation of the experimental observations. The observed temperature effect suggests that conformational flexibility plays a role in nucleotide incorporation and bypass fidelity opposite 10S-(+)-trans-anti-[benzo[a]pyrene]-N2-dG by Dpo4
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: ATP binding to replication factor C is sufficient for loading the heterotrimeric PCNA123 [proliferating cell nuclear antigen (PCNA)] clamp onto DNA that includes a rate-limiting conformational rearrangement of the complex. ATP hydrolysis is required for favorable recruitment and interactions with the replication polymerase (PolB1) that most likely include clamp closing and dissociation of replication factor C. Surprisingly, the assembled holoenzyme complex synthesizes DNA distributively and with low processivity, unlike most other well-characterized DNA polymerase holoenzyme complexes. PolB1 repeatedly disengages from the DNA template, leaving PCNA123 behind. Interactions with a C-terminal PCNA-interacting peptide (PIP) motif on PolB1 specifically with PCNA2 are required for holoenzyme formation and continuous re-recruitment during synthesis
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the conformational dynamics of the Y-family DNA polymerase Dpo4 on DNA is characterized in real time using single-molecule Förster resonance energy transfers (mFRET). Two different binary complexes consistent with DNA translocation in the polymerase active site
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme bypasses Pt-GG DNA (1,2-intrastrand covalent linkage, cis-Pt-1,2-d(GpG)). This is a dynamic process, in which the lesion is converted from an open and angular conformation at the first insertion to a depressed and nearly parallel conformation at the subsequent reaction stages to fit into the active site of Dpo4
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: Dpo4 predominantly uses a template slippage deletion mechanism when replicating repetitive DNA sequences. Dpo4 stabilizes the skipped template base in an extrahelical conformation between the polymerase and the little-finger domains of the enzyme
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the fidelity of Dpo4 is in the range of 0.001-0.0001. The ground-state binding affinity of correct nucleotides is 10-50-fold weaker than those of replicative DNA polymerases. The affinity of incorrect nucleotides for Dpo4 is about 2-10-fold weaker than that of correct nucleotides. The mismatched dCTP has an affinity similar to that of the matched nucleotides when it is incorporated against a pyrimidine template base flanked by a 5'-template guanine. The mismatch incorporation rates, regardless of the 5'-template base, are about 2-3 orders of magnitude slower than the incorporation rates for matched nucleotides, which is the predominant contribution to the fidelity of Dpo4
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: replication bypass studies in vitro reveal that the polymerase inserts dNTPs opposite the (6S,8R,11S)-trans-4-hydroxynonenal-1,N2-dGuo adduct in a sequence-specific manner. If the template 5'-neighbor base is dCyt, the polymerase inserts primarily dGTP. If the template 5'-neighbor base is dThy, the polymerase inserts primarily dATP
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme does not efficiently insert nucleotides opposite to the (6S,8R,11S)-1,N2-deoxyguanosine adduct, consistent with the low levels of Gua->Thy mutations. However it extends past the (6S,8R,11S)-1,N2-deoxyguanosine:dCyd pair. A series of ternary (Dpo4-DNA-dNTP) structures with (6S,8R,11S)-1,N2-deoxyguanosine-adducted templates suggest that during replication, the ring-closed (6S,8R,11S)-1,N2-deoxyguanosine lesion at the active site hinders incorporation of dNTPs opposite the lesion, whereas the ring-opened form of the lesion in the (6S,8R,11S)-1,N2-deoxyguanosine:dCyd pair allows for extension to full-length product
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: proliferating cell nuclear antigen facilitates DNA synthesis with Dpo3, as with Dpo1 and Dpo4, but very weakly with Dpo2. DNA synthesis in the presence of proliferating cell nuclear antigen, replication factor C, and single-stranded binding protein is most processive with DNA polymerase Dpo1 in comparison to DNA polymerase Dpo3 and Dpo4. DNA lesion bypass DNA synthesis in the presence of proliferating cell nuclear antigen, replication factor C, and single-stranded binding protein is most effective with DNA polymerase Dpo4 in comparison to DNA polymerase Dpo1 and Dpo3. Both Dpo2 and Dpo3, but not Dpo1, bypass hypoxanthine and 8-oxoguanine. Dpo2 and Dpo3 bypass uracil and cis-syn cyclobutane thymine dimer, respectively. DNA polymerase Dpo2 and Dpo3 possess very low DNA polymerase and 3' to 5' exonuclease activities in vitro compared with Dpo1 and Dpo4
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: in addition to the correct insertion of dCTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: dTTP incorporation is the most preferred addition opposite the N6dA-(OH)2butyl-GSH adduct, N6dA-butanetriol adduct, or unmodified dA
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the rate of mismatched nucleotide incorporation is greater than the rate of correct dC insertion at 55 °C, whereas at 37 °C there is little selectivity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: incorporated of 2-amino-3-methylimidazo[4,5-f]quinoline C8- and N2-dGuo adducts into the G1- and G3-positions of the NarI recognition sequence (5'-G1G2CG3CC-3'), which is a hotspot for arylamine modification. Replication of the C8-adduct at the G3-position results in two-base deletion, whereas error-free bypass and extension is observed at the G1-position. The N2-adduct is bypassed and extended when positioned at the G1-position, and the error-free product is observed. The N2-adduct at the G3-position is more blocking and is bypassed and extended only by Dpo4 to produce an errorfree product. The replication of the 2-amino-3-methylimidazo[4,5-f]quinoline-adducts of dGuo is strongly influenced by the local sequence and the regioisomer of the adduct
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the initial enzyme/DNA/dNTP complex undergoes a rapid (18/s), reversible (21/s) conformational change, followed by relatively rapid phosphodiester bond formation (11/s) and then fast release of pyrophosphate, followed by a rate-limiting relaxation of the active conformation (2/s) and then rapid DNA release, yielding an overall steady-state kcat of less than 1/s
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: removal of the 2-amino group from the template dG (i.e. deoxyinosine) has little impact on the catalytic efficiency of either polymerase, although the misincorporation frequency is increased by an order of magnitude. Deoxyxanthosine is highly miscoding with both polymerases, and incorporation of several bases is observed. The addition of bromine or oxygen at C2 lowers the Tm further, strongly inhibits and increases the frequency of misincorporation
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: ring-opening of the 3-(2'-deoxy-beta-D-erythro-pentofuranosyl)-5,6,7,8-tetrahydro-8-hydroxypyrimido[1,2-a] purin-10(3H)-one adduct promotes error-free bypass by the Sulfolobus solfataricus DNA polymerase Dpo4
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme inefficiently bypasses (5'S)-8,5'-cyclo-2'-deoxyguanosine with dCTP preferably incorporated and dATP misincorporated. (5'S)-8,5'-cyclo-2'-Deoxyguanosine attenuates K(d,dNTP,app) and k(pol)
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme inefficiently bypasses (5'S)-8,5'-cyclo-2'-deoxyguanosine with dCTP preferably incorporated and dTTP misincorporated. The (5'S)-8,5'-cyclo-2'-Deoxyguanosine-adduct-duplex complex causes 6fold decrease in Dpo4:DNA binding affinity, and significantly reduces the concentration of the productive Dpo4:DNA:dCTP complex
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: template specificity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 3'--5' activity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 3'--5' activity, identical to RTHI nuclease
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: role in non-homologous end joining of double strand breaks, perhaps including those with damaged ends, possible role for pol IV in base excision repair
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the enzyme has intrinsic 5'-2-deoxyribose-5-phosphate lyase activity. Pol IV has low processivity and can fill short gaps in DNA. The gap-filling activity of pol IV is not enhanced by a 5'-phosphate on the downstream primer but is stimulated by a 5'-terminal synthetic abasic site. Pol IV incorporates rNTPs into DNA with high efficiency relative to dNTPs. Pol IV is highly inaccurate, with an unusual error specificity indicating the ability to extend primer termini with limited homology
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: double-stranded DNA property of DNA polymerase epsilon is required for epigenetic silencing at telomeres
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: enzyme has two exonuclease 3'--5' degradative activities: an exonuclease activity and an inorganic diphosphate-dependent degradative activity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: 44kDa C-terminal fragment has no exonuclease activity, reduced efficiency with Mn2+ and reduced capacity to initiate terminal protein-primed DNA replication
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: Phi29 DNA polymerase belongs to the family B DNA polymerases able to start replication by protein-priming
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: phi29 DNA polymerase accomplishes sequential template-directed addition of dNMP units onto the 3'-OH group of a growing DNA chain, in addition phi29 DNApol catalyses 3'-5' exonucleolysis, that is, the release of dNMP units from the 3' end of a DNA strand
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 5'--3' activity, pol I
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme can traverse a wide variety of DNA lesions. The enzyme is moderately processive. It can substitute for Taq in polymerase chain reaction (PCR) and can bypass DNA lesions that normally block Taq
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the flexibility on the template side of the Dbh active site allows for a consistent location of the incoming dNTP regardless of whether or not it is correctly paired with its templating partner. Contact of the dNTP sugar with the Phe12 steric gate side chain is maintained in all circumstances with the result that Dbh shows stringent discrimination against ribonucleotides but does not use the steric gate side chain as a discriminator against nascent mispairs
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: at optimal temperature (70-75°C) a singly primed, single-stranded recombinant phage M13 DNA is efficiently replicated in ten min using a ratio of enzyme molecule to primed-template of 0.8
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the activated herring sperm DNA is an optimal template and gives 3times higher activity than that obtained with poly(dA)/oligo(dT). The DNA polymerase can not use templates without primer (poly(dA) and poly(dT)), even when appropriate priming ribonucleotides (UTP or ATP, respectively) are supplied. It does not accept a polyribonucleotide template (poly(rA):oligo(dT))
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: DNA polymerase Dpo4 can replicate past a variety of DNA lesions. When replicating undamaged DNA, the enzyme is prone to make base pair substitutions
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: activity with poly(dA) or poly(dT) as template, minimal primers are dAMP or dTMP. Lengthening of primers by each mononucleotide increases their affinity about 2.16fold. The affinity of the primer d(pA)gp(rib*) with a deoxyribosylurea residue at the 3'-end does not differ essentially from that of d(pA)9. Substitution of the 3'-terminal nucleotide of a complementary primer for a noncomplementary nucleotide, e.g., substitution of 3'-terminal A for C in d(pA)10 in the reaction catalyzed on poly(dT), decreases the affinity of a primer by one order of magnitude
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: most of the dNTP analogs with modified sugar moiety tested are shown to be specific terminating substrates for the synthesis irreversibly blocking further elongation of a nascent chain. The most powerful inhibitors are the 3'-amino derivatives of deoxy and arabino nucleoside triphosphates, while specific reverse transcriptase inhibitors, 3'-azido and 3'-methoxy derivatives of dNTP, were found to be inactive
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the activated herring sperm DNA is an optimal template and gives 3times higher activity than that obtained with poly(dA)/oligo(dT). The DNA polymerase can not use templates without primer (poly(dA) and poly(dT)), even when appropriate priming ribonucleotides (UTP or ATP, respectively) are supplied. It does not accept a polyribonucleotide template (poly(rA):oligo(dT))
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: DNA polymerase Dpo4 can replicate past a variety of DNA lesions. When replicating undamaged DNA, the enzyme is prone to make base pair substitutions
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme can traverse a wide variety of DNA lesions. The enzyme is moderately processive. It can substitute for Taq in polymerase chain reaction (PCR) and can bypass DNA lesions that normally block Taq
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: calf thymus DNA
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme can traverse a wide variety of DNA lesions. The enzyme is moderately processive. It can substitute for Taq in polymerase chain reaction (PCR) and can bypass DNA lesions that normally block Taq
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: nicked duplex is no substrate of phage T4-induced DNA polymerase
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: template specificity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time, cannot initiate a chain de novo, requires a primer which may be DNA or RNA
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 3'--5', phage T4-induced DNA polymerase
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: primed single strands
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: preferentially removes purines opposite an abasic site
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 3'--5' activity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease activity utilizes both, ssDNA and melted dsDNA templates, mismatched basepair is preferred over a correct basepair, removes an incorrect base incorporated opposite a template lesion
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 3'--5', phage T4-induced DNA polymerase
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease activity contributes to the avoidance of alkylation mutations
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: phage T4 DNA polymerase is essential for initiation and maintenance of viral DNA replication
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: bacteriohage T4 and bacteriophage RB69 replicative DNA polymerases exhibit differing abilities to form various base pairs. Formation of Watson-Crick base pairs occurs at similar rates between the two proteins but the incoming nucleotides are bound less tightly by RB69 DNA polymerase. Incorporation of an A opposite furan by T4 DNA polymerase is more rapid than for RB69 DNA polymerase with the two proteins having similar binding constants for the incoming dATP. An A:C mismatch is formed almost equally well by both proteins, while a significant difference exists when a T:T mismatch is formed
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: T4 DNA polymerase can remove two incorrect nucleotides under single turnover conditions, which includes presumed exonuclease-to-polymerase and polymerase-to-exonuclease active site switching steps and proofreading reactions that initiate in the polymerase active center are not intrinsically processive
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 3'--5' and 5'--3' activity activity, phage T5-induced DNA polymerase
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: phage T5-induced DNA polymerase
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time, cannot initiate a chain de novo, requires a primer which may be DNA or RNA
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Testudines agrionemys
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: PI-TfuI recognizes a minimal sequence of 16 base pairs, PI-TfuII requires a sequence of 21 base pairs, both enzymes have endonuclease activity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the DNA polymerase also shows 3'-5' exonuclease activity. The 3'5' exonuclease activity of the DNA polymerase is important for DNA elongation with high fidelity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the enzyme readily bypasses N2-methyl(Me)G and O6-MeG, but is strongly blocked at O6-benzyl(Bz)G and N2-BzG. the enzyme shows 110-, 180-, and 300fold decreases in catalytic efficiency (kcat/Km) for nucleotide insertion opposite an abasicP site, N2-MeG, and O6-MeG but 1800- and 5000fold decreases opposite O6-BzG and N2-BzG, respectively, as compared to G. DNA polymerase Vent (exo-) from Thermococcus litoralis is as or more efficient as polymerase Dpo4 from Sulfolobus solfataricus in synthesis opposite O6-MeG and AP lesions, whereas DNA polymerase Dpo4 from Sulfolobus solfataricus is much or more efficient opposite N2-alkylGs than DNA polymerase Vent (exo-) from Thermococcus litoralis, irrespective of DNA-binding affinity. DNA polymerase Vent (exo-) accepts nonbulky DNA lesions (e.g., N2- or O6-MeG and an AP site) as manageable substrates despite causing errorprone synthesis
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: activity with poly(dA) or poly(dT) as template, minimal primers are dAMP or dTMP. Lengthening of primers by each mononucleotide increases their affinity about 2.16fold. The affinity of the primer d(pA)gp(rib*) with a deoxyribosylurea residue at the 3'-end does not differ essentially from that of d(pA)9. Substitution of the 3'-terminal nucleotide of a complementary primer for a noncomplementary nucleotide, e.g., substitution of 3'-terminal A for C in d(pA)10 in the reaction catalyzed on poly(dT), decreases the affinity of a primer by one order of magnitude
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: wild-type enzyme, but not the truncated form has exonuclease 5'--3' activity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Thermus aquaticus INValphaF''
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 5'--3' activity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: no exonuclease 3'--5' activity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease 5'--3' activity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: no exonuclease 3'--5' activity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: enzyme also has RNAse H/exonuclease 5'--3' activity, enzyme prefers RNA/DNA substrate over DNA/DNA duplex
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: several dTTP analoges bearing a photoreactive 2-nitro-5-azidobenzoyl group attached at position 5 of uracil through linkers of various lengths, are substrates in the elongation reaction of the 5'-32P-labeled primer-template complex. The incorporation of the analogs into the 3' primer end did not impede further elongation of the chain in the presence of natural dNTP
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: in the presence of Mg2+ or Mn2+, the POLX catalytic domain inserts dIMP, IMP and 8-oxo-dGMP opposite deoxycytosine as well as dGMP and GMP, PolX likely prefers deoxyguanine to deoxythymidine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: DNA-dependent DNA polymerase activity to incorporate dNTP into gapped M13mp2 DNA
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: several dTTP analoges bearing a photoreactive 2-nitro-5-azidobenzoyl group attached at position 5 of uracil through linkers of various lengths, are substrates in the elongation reaction of the 5'-32P-labeled primer-template complex. The incorporation of the analogs into the 3' primer end did not impede further elongation of the chain in the presence of natural dNTP
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
Substrates: in the presence of Mg2+ or Mn2+, the POLX catalytic domain inserts dIMP, IMP and 8-oxo-dGMP opposite deoxycytosine as well as dGMP and GMP, PolX likely prefers deoxyguanine to deoxythymidine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: DNA-dependent DNA polymerase activity to incorporate dNTP into gapped M13mp2 DNA
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA substrate: gapped duplex or single-stranded 5'-ends smaller than 100 nucleotides, pol I, pol II and pol III
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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Substrates: overview: physiological roles in replication and in DNA repair synthesis
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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Substrates: DNA polymerase gamma: required for mitochondrial DNA replication but encoded in the nucleus
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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Substrates: template specificity
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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dGTP + DNAn
?
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Substrates: Dbh is a distributive enzyme showing a low DNA and nucleotide binding affinity along with a slow polymerization rate. DNA binding occurs in a single step, diffusion-controlled manner. The rate-limiting step of nucleotide incorporation (correct and incorrect) is the chemical step (phosphoryl transfer) and not a conformational change of the enzyme. An induced fit mechanism to select and incorporate nucleotides during DNA polymerization can not be detected for the enzyme
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dGTP + DNAn
?
Substrates: in addition to the correct insertion of dGTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
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dGTP + DNAn
?
Substrates: -
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dGTP + DNAn
?
Substrates: in addition to the correct insertion of dGTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
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dGTP + DNAn
diphosphate + DNAn+1
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Substrates: systematic determination of the single-turnover incorporation kinetics of all four native nucleotides and a set of Cy3-labeled nucleotides by the Klenow fragment of Escherichia coli DNA polymerase I
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dGTP + DNAn
diphosphate + DNAn+1
-
Substrates: -
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dGTP + DNAn
diphosphate + DNAn+1
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Substrates: with activated calf thymus DNA
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dGTP + DNAn
diphosphate + DNAn+1
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Substrates: dNTP insertion opposite a benzo[a]pyrene-N2-dG-adduct
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DNA 21/41-mer + dTTP
? + diphosphate
Substrates: kinetic mechanism for DNA polymerization is proposed, the enzyme utilizes an induced-fit mechanism to select correct incoming nucleotides
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DNA 21/41-mer + dTTP
? + diphosphate
Substrates: kinetic mechanism for DNA polymerization is proposed, the enzyme utilizes an induced-fit mechanism to select correct incoming nucleotides
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dNTP + DNAn
diphosphate + DNAn+1
Substrates: -
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dTTP + DNAn
?
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Substrates: Dbh is a distributive enzyme showing a low DNA and nucleotide binding affinity along with a slow polymerization rate. DNA binding occurs in a single step, diffusion-controlled manner. The rate-limiting step of nucleotide incorporation (correct and incorrect) is the chemical step (phosphoryl transfer) and not a conformational change of the enzyme. An induced fit mechanism to select and incorporate nucleotides during DNA polymerization can not be detected for the enzyme
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dTTP + DNAn
?
Substrates: in addition to the correct insertion of dTTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
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dTTP + DNAn
?
Substrates: dTTP incorporation is the most preferred addition opposite the N6dA-(OH)2butyl-GSH adduct, N6dA-butanetriol adduct, or unmodified dA
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dTTP + DNAn
?
Substrates: dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2-deoxyribofuranosid-5-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
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dTTP + DNAn
?
Substrates: -
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dTTP + DNAn
?
Substrates: in addition to the correct insertion of dTTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
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dTTP + DNAn
?
Substrates: dTTP incorporation is the most preferred addition opposite the N6dA-(OH)2butyl-GSH adduct, N6dA-butanetriol adduct, or unmodified dA
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dTTP + DNAn
?
Substrates: dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2-deoxyribofuranosid-5-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
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dTTP + DNAn
?
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Substrates: activity with poly(dA) or poly(dT) as template, minimal primers are dAMP or dTMP. Lengthening of primers by each mononucleotide increases their affinity about 2.16-fold. The affinity of the primer d(pA)gp(rib*) with a deoxyribosylurea residue at the 3'-end does not differ essentially from that of d(pA)9. Substitution of the 3'-terminal nucleotide of a complementary primer for a noncomplementary nucleotide, e.g., substitution of 3'-terminal A for C in d(pA)10 in the reaction catalyzed on poly(dT), decreases the affinity of a primer by one order of magnitude
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dTTP + DNAn
?
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Substrates: activity with poly(dA) or poly(dT) as template, minimal primers are dAMP or dTMP. Lengthening of primers by each mononucleotide increases their affinity about 2.16-fold. The affinity of the primer d(pA)gp(rib*) with a deoxyribosylurea residue at the 3'-end does not differ essentially from that of d(pA)9. Substitution of the 3'-terminal nucleotide of a complementary primer for a noncomplementary nucleotide, e.g., substitution of 3'-terminal A for C in d(pA)10 in the reaction catalyzed on poly(dT), decreases the affinity of a primer by one order of magnitude
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dTTP + DNAn
diphosphate + DNAn+1
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Substrates: systematic determination of the single-turnover incorporation kinetics of all four native nucleotides and a set of Cy3-labeled nucleotides by the Klenow fragment of Escherichia coli DNA polymerase I
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dTTP + DNAn
diphosphate + DNAn+1
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Substrates: with labeled 20/33-mer primer-template duplex DNA
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dTTP + DNAn
diphosphate + DNAn+1
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Substrates: activity assay with plus-strand m13 DNA annealed to 5'-32P end-labeled primer 5'-GCTGTTGGGAAGGGCGATCG-3'
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dTTP + DNAn
diphosphate + DNAn+1
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Substrates: with activated calf thymus DNA
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dTTP + DNAn
diphosphate + DNAn+1
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Substrates: dNTP insertion opposite a benzo[a]pyrene-N2-dG-adduct
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dTTP + DNAn
diphosphate + DNAn+1
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Substrates: incorporation of dTTP into poly(rA)-p(dT)45
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dTTP + DNAn
diphosphate + DNAn+1
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Substrates: incorporation of dTTP into poly(rA)-p(dT)45
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dTTP + DNAn
diphosphate + DNAn+1
Substrates: incorporation of dTTP into poly(rA)-p(dT)45
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dTTP + DNAn
diphosphate + DNAn+1
Substrates: incorporation of dTTP into poly(rA)-p(dT)45
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N1-methyl-2'-deoxyadenosine 5'-triphosphate + DNAn
diphosphate + ?
Substrates: -
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N1-methyl-2'-deoxyadenosine 5'-triphosphate + DNAn
diphosphate + ?
Substrates: -
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North-methanocarba-dATP + DNAn
?
Substrates: the role of sugar geometry during nucleotide selection is probed by the enzyme from Sulfolobus solfataricus using fixed conformation nucleotide analogues. The enzyme preferentially inserts North-methanocarba-dATP that locks the central ring into a RNA-type (C2'-exo, North) conformation near a C3'-endo pucker compared to a South-methanocarba-dATP that locks the central ring system into a (C3'-exo, South) conformation near a C2'-endo pucker
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North-methanocarba-dATP + DNAn
?
Substrates: the role of sugar geometry during nucleotide selection is probed by the enzyme from Sulfolobus solfataricus using fixed conformation nucleotide analogues. The enzyme relatively tolerant to the substrate conformation: North-methanocarba-dATP that locks the central ring into a RNA-type (C2'-exo, North) conformation near a C3'-endo pucker or South-methanocarba-dATP that locks the central ring system into a (C3'-exo, South) conformation near a C2'-endo pucker
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North-methanocarba-dATP + DNAn
?
Substrates: the role of sugar geometry during nucleotide selection is probed by the enzyme from Sulfolobus solfataricus using fixed conformation nucleotide analogues. The enzyme preferentially inserts North-methanocarba-dATP that locks the central ring into a RNA-type (C2'-exo, North) conformation near a C3'-endo pucker compared to a South-methanocarba-dATP that locks the central ring system into a (C3'-exo, South) conformation near a C2'-endo pucker
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North-methanocarba-dATP + DNAn
?
Substrates: the role of sugar geometry during nucleotide selection is probed by the enzyme from Sulfolobus solfataricus using fixed conformation nucleotide analogues. The enzyme relatively tolerant to the substrate conformation: North-methanocarba-dATP that locks the central ring into a RNA-type (C2'-exo, North) conformation near a C3'-endo pucker or South-methanocarba-dATP that locks the central ring system into a (C3'-exo, South) conformation near a C2'-endo pucker
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South-methanocarba-dATP + DNAn
?
Substrates: the role of sugar geometry during nucleotide selection is probed by the enzyme from Sulfolobus solfataricus using fixed conformation nucleotide analogues. The enzyme relatively tolerant to the substrate conformation: North-methanocarba-dATP that locks the central ring into a RNA-type (C2'-exo, North) conformation near a C3'-endo pucker or South-methanocarba-dATP that locks the central ring system into a (C3'-exo, South) conformation near a C2'-endo pucker
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South-methanocarba-dATP + DNAn
?
Substrates: the role of sugar geometry during nucleotide selection is probed by the enzyme from Sulfolobus solfataricus using fixed conformation nucleotide analogues. The enzyme relatively tolerant to the substrate conformation: North-methanocarba-dATP that locks the central ring into a RNA-type (C2'-exo, North) conformation near a C3'-endo pucker or South-methanocarba-dATP that locks the central ring system into a (C3'-exo, South) conformation near a C2'-endo pucker
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additional information
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Substrates: the enzyme also displays 3'5'-exonuclease activity
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additional information
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Substrates: the R2 polymerase can utilize both RNA and DNA templates, but the processivity of the enzyme on single stranded DNA templates is higher than its processivity on RNA templates, R2-RT is also capable of synthesizing the second DNA strand during retrotransposition
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additional information
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Substrates: single-strand-dependent and double-strand-dependent 3'-5' exonuclease activity and marginal 5'-3' exonuclease activity
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additional information
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Substrates: small 4'-methyl and -ethyl modifications of the nucleoside triphosphate do not perturb Klenow fragment catalysis
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additional information
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Substrates: Pol beta does incorporate size augmented thymidine analogues besides the unmodified TTP
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additional information
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Substrates: PolH can be up-regulated by DNA breaks induced by ionizing radiation or chemotherapeutic agents, and knockdown of PolH gives cells resistance to apoptosis induced by DNA breaks in multiple cell lines and cell types in a p53-dependent manner. PolH has a role in the DNA damage checkpoint. POlH is target of p53
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additional information
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Substrates: modifying the beta,gamma leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity, and the catalytic mechanism of DNA polymerase
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additional information
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Substrates: all pols exclusively promote misincorporation of dCMP opposite a 2'-deoxyinosine lesion during translesion synthesis, isozymes pol alpha, pol eta, and pol kappaDELTAC promote preferential incorporation of 2'-deoxycytidine monophosphate , the wrong base, opposite a 2'-deoxyinosine lesion, no incorporation of 2'-deoxythymidine monophosphate, the correct base, is observed opposite the lesion
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additional information
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Substrates: (2R,4R)-4-(2-amino-6-oxo-9H-purin-9-yl)-1,3-dioxolan-2-yl-methanol triphosphate and 2',3'-dideoxy-2',3'-didehydroguanoside triphosphate, and carbovir triphosphate are much less efficiently incorporated than the natural deoxynucleoside triphosphate dGTP
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additional information
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Substrates: while small 4'-methyl and -ethyl modifications of the nucleoside triphosphate perturb Pol beta catalysis, extension of modified primer strands is only marginally affected
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additional information
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Substrates: Pol beta does not incorporate size augmented thymidine analogues, while the unmodified TTP is processed
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additional information
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Substrates: the excision of the matched 3'-monophosphorylated form of 2'-deoxy-2',2'-difluorocytidine moiety by the wild type pol gamma is 55fold slower than the excision of matched 3'-dCMP
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additional information
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Substrates: comparing RNA primer-templates and DNA primer templates of identical sequence show that herpes polymerase greatly prefers to elongate the DNA primer by 650-26000fold, thus accounting for the extremely low efficiency with which herpes polymerase elongates primase-synthesized primers
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additional information
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Substrates: Neq L and Neq S are needed to form the active DNA polymerase that possesses higher proofreading activity. The genetically protein splicing-processed Neq P shows the same properties as the protein trans-spliced Neq C
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additional information
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Substrates: the enzyme is responsible for mutagenesis, e.g. UV-induced, in human host cells of lungs of cystic fibrosis patients contributing to morbidity and mortality of these people, with a striking correlation between mutagenesis and the persistence of Pseudomonas aeruginosa, mechanisms of mutagenesis, enzyme regulation, overview, the enzyme is responsible for resistance to to nitrofurazone and 4-nitroquinoline-1-oxide toxification
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additional information
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Substrates: DNA synthesis on M13Gori single-stranded phage DNA as template DNA
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additional information
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Substrates: the enzyme causes 1-bp deletions and different base substitutions in plasmids pKTpheA56+A and pKTpheA22TAG, pKTpheA22TAA, and pKTpheA22TGA, respectively, in stationary cells, overview, Pol IV-dependent mutagenesis causes an approximately 10fold increase in the frequency of accumulation of 1-bp deletion mutations on selective plates in wild-type populations starved for more than 1 week, development of a mutant detection assay system allowing to separately detect the mutants, no effect of Pol IV on the frequency of accumulation of base substitution mutations in starving cells is observed, overview, RecA independence of Pol IV-associated mutagenesis mechanisms different from the classical RecA-dependent SOS response can elevate Pol IV-dependent mutagenesis in starving cells, overview
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additional information
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Substrates: primer ssM13 DNA is the preferred substrate
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additional information
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Substrates: primer ssM13 DNA is the preferred substrate
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additional information
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Substrates: DNA polymerase switching mechanism by which PabPol B displaces PabPol D from proliferating cell nuclear antigen on the DNA duplex
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additional information
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Substrates: DNA polymerases PolB and PolD slip in vitro on a template that consists of single-stranded DNA (ssDNA) with a hairpin structure flanked by short direct repeats. Pyrococcus abyssi proliferating cell nuclear antigen increases replication fidelity of this template
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additional information
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Pyrococcus abyssi GE5 / CNCM I-1302 / DSM 25543
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Substrates: DNA polymerase switching mechanism by which PabPol B displaces PabPol D from proliferating cell nuclear antigen on the DNA duplex
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additional information
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Substrates: polymerase binds DNA containing uracil 1.54.5-fold more strongly than hypoxanthine
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additional information
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Substrates: the enzyme has strong 3'->5' exonucleolytic activity and has a template-primer preference which is characteristic of a replicative DNA polymerase
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additional information
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Substrates: the enzyme has strong 3'->5' exonucleolytic activity and has a template-primer preference which is characteristic of a replicative DNA polymerase
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additional information
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Substrates: FEN-1 has both 5'-flap endonuclease and 5'3' exonuclease activities, FEN-1 activity is elevated by the presence of a 1 nucleotide expansion at the 3' end in the upstream primer of substrates called: structures with a 1 nt 3'-flap, which appear to be the most preferable substrates for FEN-1. Serial intermediates with a 1 nt 3'-flap and 5' variable-length flaps are formed by cooperative functioning of Pyrococcus horikoshii FEN-1 with either B or D DNA polymerases
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additional information
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Substrates: FEN-1 has both 5'-flap endonuclease and 5'3' exonuclease activities, FEN-1 activity is elevated by the presence of a 1 nucleotide expansion at the 3' end in the upstream primer of substrates called: structures with a 1 nt 3'-flap, which appear to be the most preferable substrates for FEN-1. Serial intermediates with a 1 nt 3'-flap and 5' variable-length flaps are formed by cooperative functioning of Pyrococcus horikoshii FEN-1 with either B or D DNA polymerases
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additional information
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Substrates: FEN-1 has both 5'-flap endonuclease and 5'3' exonuclease activities, FEN-1 activity is elevated by the presence of a 1 nucleotide expansion at the 3' end in the upstream primer of substrates called: structures with a 1 nt 3'-flap, which appear to be the most preferable substrates for FEN-1. Serial intermediates with a 1 nt 3'-flap and 5' variable-length flaps are formed by cooperative functioning of Pyrococcus horikoshii FEN-1 with either B or D DNA polymerases
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additional information
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Substrates: at low pH the chemical step is rate limiting for catalysis, but at high pH, a postchemistry conformational step is rate limiting due to a pH-dependent increase in the rate of nucleotidyl transfer
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additional information
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Substrates: lesion-bypass DNA polymerase
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additional information
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Substrates: the widely used anticancer drug, cis-diamminedichloroplatinum(II), i.e. cisplatin, reacts with adjacent purine bases in DNA to form predominantly cis-[Pt(NH3)2(d(GpG)-N7(1),-N7(2))] intrastrand cross-links, DNA polymerase IV is able to perform translesion synthesis in the presence of DNA-distorting damage such as cisplatin-DNA adducts, overview
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additional information
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Substrates: replication cycle of Dpo4, and induced fit and translocation mechanisms, overview
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additional information
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Substrates: replication cycle of Dpo4, and induced fit and translocation mechanisms, overview
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additional information
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Substrates: Dpo4 utilizes an induced-fit mechanism to select correct incoming nucleotides at 37°C, overview
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additional information
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Substrates: potential structures of purine-purine base pairs, overview
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additional information
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Substrates: simulation model of the solvated Dpo4/DNA/8-oxoG:dCTP complex, catalytic site structure, overview
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additional information
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Substrates: significant preferential dATP insertion, dATP can be misincorporated opposite the benzo[a]pyrene-derived N2-dG adduct, standing-start single-nucleotide insertion assays, overview
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additional information
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Substrates: significant preferential dATP insertion, dATP can be misincorporated opposite the benzo[a]pyrene-derived N2-dG adduct, standing-start single-nucleotide insertion assays, overview
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additional information
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Substrates: Dpo4 produces mismatch and frameshift mutations at benzo[a]pyrene-derived lesions, overview
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additional information
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Substrates: Dpo4 produces mismatch and frameshift mutations at benzo[a]pyrene-derived lesions, overview
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additional information
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Substrates: simulations, based on crystal complexes of Dpo4 are performed, exploring possible transitions and mechanisms associated with Dpo4s catalytic cycle. Dynamics simulations before the nucleotidyl-transfer reaction and simulations after the reaction are performed. Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2 DNA polymerase IV may accommodate lesion bypass
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additional information
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Substrates: the DNA lesion bypass polymerase can bind up to eight base pairs of double-stranded DNA which is entirely in B-type. Thus, the DNA binding cleft of Dpo4 is flexible and can accommodate both A- and B-type oligodeoxyribonucleotide duplexes as well as damaged DNA
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additional information
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Substrates: Dpo3 has an active exonuclease proofreading domain, it shows intrinsic exonuclease activity
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additional information
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Substrates: Dpo3 has an active exonuclease proofreading domain, it shows intrinsic exonuclease activity
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additional information
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Substrates: simulations, based on crystal complexes of Dpo4 are performed, exploring possible transitions and mechanisms associated with Dpo4s catalytic cycle. Dynamics simulations before the nucleotidyl-transfer reaction and simulations after the reaction are performed. Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2 DNA polymerase IV may accommodate lesion bypass
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additional information
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Substrates: the DNA lesion bypass polymerase can bind up to eight base pairs of double-stranded DNA which is entirely in B-type. Thus, the DNA binding cleft of Dpo4 is flexible and can accommodate both A- and B-type oligodeoxyribonucleotide duplexes as well as damaged DNA
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additional information
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Substrates: Dpo3 has an active exonuclease proofreading domain, it shows intrinsic exonuclease activity
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additional information
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Substrates: Szi DNA polymerase possesses associated 3'-5' and 5'-3' exonuclease activities
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additional information
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Substrates: the E664 residue (located in thumb domain) acts as a steric gate, which is involved in recognition of the DNA substrate by the enzyme
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additional information
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Substrates: the DNA polymerase gene of Thermococcus marinus contains an intein inserted at the pol-b site
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additional information
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Substrates: the DNA polymerase possesses a 3'->5' exonuclease activity
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additional information
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Substrates: the DNA polymerase possesses a 3'->5' exonuclease activity
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additional information
?
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Substrates: the enzyme also posseses 3'->5' exonuclease activity
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additional information
?
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Substrates: the enzyme also posseses 3'->5' exonuclease activity
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additional information
?
-
-
Substrates: a 3'->5' exonuclease activity is associated with the purified DNA polymerase
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additional information
?
-
Substrates: DNA-dependent DNA polymerase commonly accepts DNA and dNTP and excludes RNA and rNTP, but some enzyme mutants also show RNA-dependent DNA polymerase activity as reverse transcriptases, overview. Reverse transcriptase is the enzyme that catalyzes DNA polymerization using RNA as a template, i.e. RNA-dependent DNA polymerase, see for EC 2.7.7.49
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additional information
?
-
-
Substrates: only the enzyme mutant T326A/L324A/Q384A/F388A/m4008A/Y438A shows RNA-dependent DNA polymerase activity, EC 2.7..7.49
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additional information
?
-
-
Substrates: only the enzyme mutant T326A/L324A/Q384A/F388A/m4008A/Y438A shows RNA-dependent DNA polymerase activity, no activity with the wild-type enzyme
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?
additional information
?
-
Substrates: DNA-dependent DNA polymerase commonly accepts DNA and dNTP and excludes RNA and rNTP, but some enzyme mutants also show RNA-dependent DNA polymerase activity as reverse transcriptases, overview. Reverse transcriptase is the enzyme that catalyzes DNA polymerization using RNA as a template, i.e. RNA-dependent DNA polymerase, see for EC 2.7.7.49
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?
additional information
?
-
-
Substrates: DNA-dependent DNA polymerase commonly accepts DNA and dNTP and excludes RNA and rNTP, but some enzyme mutants also show RNA-dependent DNA polymerase activity as reverse transcriptases, overview. Reverse transcriptase is the enzyme that catalyzes DNA polymerization using RNA as a template, i.e. RNA-dependent DNA polymerase, see for EC 2.7.7.49
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?
additional information
?
-
-
Substrates: only the enzyme mutant T326A/L324A/Q384A/F388A/m4008A/Y438A shows RNA-dependent DNA polymerase activity, EC 2.7..7.49
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?
additional information
?
-
-
Substrates: only the enzyme mutant T326A/L324A/Q384A/F388A/m4008A/Y438A shows RNA-dependent DNA polymerase activity, no activity with the wild-type enzyme
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?
additional information
?
-
-
Substrates: the mutant enzyme shows single deoxynucleotide additions with dCTP, dATP and dTTP, but not with dGTP as it results in addition of two successive base incorporations on the chosen template 2 hybridised to the DNA primer 1, thereby invalidating the single-turnover kinetic model, Michaelis-Menten mechanism, overview
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additional information
?
-
-
Substrates: the catalytic efficiency of PolX is almost the same with and without dNTPs, whereas that of the domain mixture increases on the addition of dNTPs
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additional information
?
-
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
Substrates: the catalytic efficiency of PolX is almost the same with and without dNTPs, whereas that of the domain mixture increases on the addition of dNTPs
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additional information
?
-
-
Substrates: the enzyme is unable to use single stranded DNA or double stranded blunt end DNA
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?
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
African swine fever virus Badajoz 1971 Vero-adapted
Substrates: -
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?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: DNA replication can be accomplished using dNDPs as substrates. In thermophiles, genome replication may be less sensitive to the energy charge of the cell than in mesophiles because thermostable polymerases can accept the diphosphorylated as well as the triphosphorylated substrates. DNA replication is thus less affected by the intracellular ATP/ADP ratio, and the relatively high efficiency with which DNA is synthesized at elevated temperatures suggests that thermophiles may be able to dispense with the triphosphorylated substrates entirely
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?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the template-dependent polymerase that can repair non-complementary DNA double strand breaks with unpaired 3' primer termini by nonhomologous end joining. Its role is to fill short gaps arising as intermediates in the process of V(D)J recombination and during processing of accidental double strand breaks
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?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
Products: -
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?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: DNA replication can be accomplished using dNDPs as substrates. In thermophiles, genome replication may be less sensitive to the energy charge of the cell than in mesophiles because thermostable polymerases can accept the diphosphorylated as well as the triphosphorylated substrates. DNA replication is thus less affected by the intracellular ATP/ADP ratio, and the relatively high efficiency with which DNA is synthesized at elevated temperatures suggests that thermophiles may be able to dispense with the triphosphorylated substrates entirely
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?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the catalytic core of yeast DNA polymerase eta prefers to incorporate dCTP opposite 7,8-dihydro-8-oxo-2'-deoxyguanosine (damage produced by reactive oxygen species in DNA). dCTP incorporation is slower than the dissociation of the polymerase from DNA. 57% of the extension products beyond the 7,8-dihydro-8-oxo-2'-deoxyguanosine are the products corresponding to the correct incorporation (C) and 43% corresponding to dATP misincorporation
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?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the catalytic core of yeast DNA polymerase eta prefers to incorporate dCTP opposite 7,8-dihydro-8-oxo-2'-deoxyguanosine (damage produced by reactive oxygen species in DNA). dCTP incorporation is slower than the dissociation of the polymerase from DNA. 57% of the extension products beyond the 7,8-dihydro-8-oxo-2'-deoxyguanosine are the products corresponding to the correct incorporation (C) and 43% corresponding to dATP misincorporation
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?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: DNA replication can be accomplished using dNDPs as substrates. In thermophiles, genome replication may be less sensitive to the energy charge of the cell than in mesophiles because thermostable polymerases can accept the diphosphorylated as well as the triphosphorylated substrates. DNA replication is thus less affected by the intracellular ATP/ADP ratio, and the relatively high efficiency with which DNA is synthesized at elevated temperatures suggests that thermophiles may be able to dispense with the triphosphorylated substrates entirely
Products: -
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?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Substrates: DNA replication can be accomplished using dNDPs as substrates. In thermophiles, genome replication may be less sensitive to the energy charge of the cell than in mesophiles because thermostable polymerases can accept the diphosphorylated as well as the triphosphorylated substrates. DNA replication is thus less affected by the intracellular ATP/ADP ratio, and the relatively high efficiency with which DNA is synthesized at elevated temperatures suggests that thermophiles may be able to dispense with the triphosphorylated substrates entirely
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: natural substrate is gapped DNA
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: polymerase I plays a role in repair of chromosomal damage
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: physiological role of pol I and pol III
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: polymerase III is necessary for DNA replication
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: polymerase alpha: role in DNA replication
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: overview: physiological roles in replication and in DNA repair synthesis
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase gamma: required for mitochondrial DNA replication but encoded in the nucleus
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: enzyme is active only in cells at meiotic prophase, in somatic cells it is in an inactive state
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase delta: with its auxiliary factor i.e. proliferating cell nuclear antigen, largely responsible for leading-strand synthesis
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: overview: physiological roles in replication and in DNA repair synthesis
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase gamma: required for mitochondrial DNA replication but encoded in the nucleus
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase alpha: with its associated primase largely responsible for lagging-strand synthesis
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: physiological role of pol I
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: physiological role of pol I, II and pol III
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: pol III can repair short gaps created by nuclease in duplex DNA, for efficient replication of the long, single-stranded templates pol III requires auxiliary subunits
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: polymerase III: role in replication of chromosomal DNA
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: polymerase II: role in DNA repair
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase V is involved in translesion synthesis and mutagenesis
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: gamma-phosphates of the incoming dNTP, contributing to charge neutralization and alignment of the alpha-phosphate for reaction
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: overview: physiological roles in replication and in DNA repair synthesis
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase gamma: required for mitochondrial DNA replication but encoded in the nucleus
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Herpes simplex virus
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: overview: functional role of mammalian DNA polymerases
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: polymerase alpha: role in DNA replication
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: polymerase beta: role in DNA repair
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase delta: with its auxiliary factor i.e. proliferating cell nuclear antigen, largely responsible for leading-strand synthesis
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: overview: physiological roles in replication and in DNA repair synthesis
Products: -
Products: -
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase gamma: required for mitochondrial DNA replication but encoded in the nucleus
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase alpha: with its associated primase largely responsible for lagging-strand synthesis
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: Pol lambda plays a role in the short-patch base excision repair rather than contributes to the long-patch base excision repair pathway
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase iota may play a limited and error-prone role in translesion synthesis across the N2-guanine adducts (possibly medium sized adducts up to N2-benzylguanine) due to the low polymerization rates and high error rates
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: role in DNA gap repair
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
Products: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: overview: functional role of mammalian DNA polymerases
Products: -
Products: -
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: overview: physiological roles in replication and in DNA repair synthesis
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: DNA polymerase gamma: required for mitochondrial DNA replication but encoded in the nucleus
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: OsPOLP1 might be involved in a repair pathway similar to long-patch base excision repair. Possible role of POLPs in plastidial DNA replication and repair
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: PabPolD might play an important role in DNA replication likely together with PabpolB, suggesting that archaea require two DNA polymerases at the replication fork
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: the enzyme has a template-primer preference which is characteristic of a replicative DNA polymerase
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the enzyme plays an essential role in DNA replication, repair, and recombination
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: polymerase alpha: role in DNA replication
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Ruellia sp.
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: -
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Substrates: two representative types of lesions: (i) 7,8-dihydro-8-oxoguanine, a small, highly prevalent lesion caused by oxidative damage; and (ii) bulky lesions derived from the environmental pre-carcinogen benzo[a]pyrene. The diol epoxide (+)-(7R,8S,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[ a]pyrene reacts largely, but not exclusively, with the exocyclic amino group of guanine to produce the major 10S (+) trans-anti-BP-N2-dG adduct, that is bypassed by Dpo4
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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Substrates: the enzyme bypasses DNA adducts pyrrolo-deoxycytosine, dP, N6-furfuryl-deoxyadenosine, and 1,N6-ethenodeoxyadenosine in a process known as translesion synthesis
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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Substrates: the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis 2-OH-dATP is predominantly incorporated opposite guanine and thymine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis. 2-OH-dATP is predominantly incorporated opposite guanine and thymine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: deamination of cytosine to uracil is a hydrolytic reaction that is greatly accelerated at high temperatures. The resulting uracil pairs with adenine during DNA replication, thereby inducing G:C to A:T transitions in the progeny. B-family DNA polymerases from hyperthermophilic archaea recognize the presence of uracil in DNA and stall DNA synthesis. Although PolB1 per se specifically binds to uracil-containing single-stranded DNA, the binding efficiency is substantially enhanced by the initiation of DNA synthesis. The generation of ds DNA is significantly inhibited, however, by the presence of template uracil. Pol B1 more efficiently recognizes uracil in DNA during DNA synthesis rather than during random diffusion in solution. Single molecules of Pol B1 bind to template uracil and stall DNA synthesis
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis 2-OH-dATP is predominantly incorporated opposite guanine and thymine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis. 2-OH-dATP is predominantly incorporated opposite guanine and thymine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis 2-OH-dATP is predominantly incorporated opposite guanine and thymine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis. 2-OH-dATP is predominantly incorporated opposite guanine and thymine
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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Substrates: role in non-homologous end joining of double strand breaks, perhaps including those with damaged ends, possible role for pol IV in base excision repair
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: double-stranded DNA property of DNA polymerase epsilon is required for epigenetic silencing at telomeres
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: exonuclease activity contributes to the avoidance of alkylation mutations
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: phage T4 DNA polymerase is essential for initiation and maintenance of viral DNA replication
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Testudines agrionemys
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Thermus aquaticus INValphaF''
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Substrates: overview: physiological roles in replication and in DNA repair synthesis
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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Substrates: DNA polymerase gamma: required for mitochondrial DNA replication but encoded in the nucleus
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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additional information
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Substrates: the R2 polymerase can utilize both RNA and DNA templates, but the processivity of the enzyme on single stranded DNA templates is higher than its processivity on RNA templates, R2-RT is also capable of synthesizing the second DNA strand during retrotransposition
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additional information
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Substrates: PolH can be up-regulated by DNA breaks induced by ionizing radiation or chemotherapeutic agents, and knockdown of PolH gives cells resistance to apoptosis induced by DNA breaks in multiple cell lines and cell types in a p53-dependent manner. PolH has a role in the DNA damage checkpoint. POlH is target of p53
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additional information
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Substrates: all pols exclusively promote misincorporation of dCMP opposite a 2'-deoxyinosine lesion during translesion synthesis, isozymes pol alpha, pol eta, and pol kappaDELTAC promote preferential incorporation of 2'-deoxycytidine monophosphate , the wrong base, opposite a 2'-deoxyinosine lesion, no incorporation of 2'-deoxythymidine monophosphate, the correct base, is observed opposite the lesion
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additional information
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Substrates: comparing RNA primer-templates and DNA primer templates of identical sequence show that herpes polymerase greatly prefers to elongate the DNA primer by 650-26000fold, thus accounting for the extremely low efficiency with which herpes polymerase elongates primase-synthesized primers
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additional information
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Substrates: Neq L and Neq S are needed to form the active DNA polymerase that possesses higher proofreading activity. The genetically protein splicing-processed Neq P shows the same properties as the protein trans-spliced Neq C
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additional information
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Substrates: the enzyme is responsible for mutagenesis, e.g. UV-induced, in human host cells of lungs of cystic fibrosis patients contributing to morbidity and mortality of these people, with a striking correlation between mutagenesis and the persistence of Pseudomonas aeruginosa, mechanisms of mutagenesis, enzyme regulation, overview, the enzyme is responsible for resistance to to nitrofurazone and 4-nitroquinoline-1-oxide toxification
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additional information
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Substrates: the widely used anticancer drug, cis-diamminedichloroplatinum(II), i.e. cisplatin, reacts with adjacent purine bases in DNA to form predominantly cis-[Pt(NH3)2(d(GpG)-N7(1),-N7(2))] intrastrand cross-links, DNA polymerase IV is able to perform translesion synthesis in the presence of DNA-distorting damage such as cisplatin-DNA adducts, overview
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additional information
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Substrates: replication cycle of Dpo4, and induced fit and translocation mechanisms, overview
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additional information
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Substrates: replication cycle of Dpo4, and induced fit and translocation mechanisms, overview
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additional information
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Substrates: the DNA polymerase gene of Thermococcus marinus contains an intein inserted at the pol-b site
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additional information
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Substrates: DNA-dependent DNA polymerase commonly accepts DNA and dNTP and excludes RNA and rNTP, but some enzyme mutants also show RNA-dependent DNA polymerase activity as reverse transcriptases, overview. Reverse transcriptase is the enzyme that catalyzes DNA polymerization using RNA as a template, i.e. RNA-dependent DNA polymerase, see for EC 2.7.7.49
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additional information
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Substrates: only the enzyme mutant T326A/L324A/Q384A/F388A/m4008A/Y438A shows RNA-dependent DNA polymerase activity, EC 2.7..7.49
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additional information
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Substrates: DNA-dependent DNA polymerase commonly accepts DNA and dNTP and excludes RNA and rNTP, but some enzyme mutants also show RNA-dependent DNA polymerase activity as reverse transcriptases, overview. Reverse transcriptase is the enzyme that catalyzes DNA polymerization using RNA as a template, i.e. RNA-dependent DNA polymerase, see for EC 2.7.7.49
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additional information
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Substrates: DNA-dependent DNA polymerase commonly accepts DNA and dNTP and excludes RNA and rNTP, but some enzyme mutants also show RNA-dependent DNA polymerase activity as reverse transcriptases, overview. Reverse transcriptase is the enzyme that catalyzes DNA polymerization using RNA as a template, i.e. RNA-dependent DNA polymerase, see for EC 2.7.7.49
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additional information
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Substrates: only the enzyme mutant T326A/L324A/Q384A/F388A/m4008A/Y438A shows RNA-dependent DNA polymerase activity, EC 2.7..7.49
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additional information
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Substrates: the catalytic efficiency of PolX is almost the same with and without dNTPs, whereas that of the domain mixture increases on the addition of dNTPs
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additional information
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Thermus thermophilus HB8 / ATCC 27634 / DSM 579
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Substrates: the catalytic efficiency of PolX is almost the same with and without dNTPs, whereas that of the domain mixture increases on the addition of dNTPs
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ca2+
Co2+
DTT
Fe2+
-
required, in [4Fe-4S] clusters, that are bound to the CysB motif in all yeast B family DNA polymerases, assembly of the essential Fe-S cluster is strictly dependent on the function of mitochondrial Nfs1 and cytosolic Nbp35. The C-terminal domain of the catalytic subunit binds the Fe-S cluster in the CysB motif requiring all Cys residues of motif Cysb
K+
KCl
Mg2+
MgCl2
Mn2+
MnCl2
-
sustitution of MgCl2 by MnCl2 produces a slight decrease of activity. Optimal activity is obtained in the presence of 0.4 mM MgCl2
Na+
NaCl
Zn2+
additional information
Ca2+
Ca2+ (but not Ba2+, Co2+, Cu2+, Ni2+, or Zn2+) is a cofactor for Dpo4-catalyzed polymerization with both native and 8-oxoG-containing DNA templates. Both dNTP and ddNTP are substrates of the polymerase in the presence of either Mg2+ or Ca2+. No pyrophosphorolysis occurs in the presence of Ca2+
Ca2+
causes a concentration-dependent shift in the translocation equilibrium, predominantly by decreasing the forward translocation rate. Decreases the dNTP dissociation rate relative to Mg2+ and increases the dNTP association rate
Co2+
can effectively replace Mg2+. When Mg2+ is replaced with Co2+, the efficiency of incorporation of dTMP opposite dA increases by 5-fold
Co2+
-
can partially replace Mg2+ in activation, optimal concentration: 2.5 mM
K+
-
pols beta, iota and zeta exhibit maximal activity under conditions of moderate KCl concentrations of 20-60 mM
K+
over 80% of maximal activity is obtained with KCl concentrations of 50-80 mM, with a maximum at 60 mM
K+
-
optimal concentration for wild-type enzyme: 50 mM, optimal concentration for G418/E507Q mutant: 100 mM
KCl
optimum salt concentration is either 50 mM KCl or 75 mM NaCl
KCl
-
increase in KCl concentration from 10 to 75 mM results in a 10fold increase in polymerase activity
Mg2+
-
binding of Mg2+-dNTP to Pol X facilitates subsequent formation of the catalytically competent Pol X-DNA-dNTP ternary complex, Pol X prefers an ordered sequential mechanism with Mg2+-dNTP as the first substrate
Mg2+
divalent cation required. Maximum activity is observed with 6 mM MgCl2, whereas about 50% activity is obtained with MnCl2 at its optimal concentration of 6 mM
Mg2+
activates, Mn2+ shows a 8.6fold higher catalytic efficiency than Mg2+
Mg2+
-
DNA polymerase alpha: increasing concentrations of Mg2+ lead to a dramatically increased affinity for poly(dT) and poly(dC) polypyrimidines, has little or no effect on the interaction of the enzyme with poly(dA)
Mg2+
-
free Mg2+ competes with primer for enzyme binding, dramatic inhibition at Mg2+ concentration above the optimum, catalytic core binds primer through a Mg2+-chelate, with each of 4 Mg2+ ions acting to coordinate 2 phosphodiester groups
Mg2+
-
synthesizes DNA processively in the presence of Mn2+ and Mg2+, optimal Mg2+ concentration is 3 mM
Mg2+
-
required, two metal ion mechanism, nucleotide binds to the enzyme as an MgdNTP-2 complex, overview. Mg2+ enforces tetrahedral geometry
Mg2+
polI activity is absolutely dependent on the presence of divalent cations Mg2+ and Mn2+, Mn2+ cannot be replaced with Mg2+ completely, optimal at 8 mM
Mg2+
-
optimal concentration for polymerase C and N2: 10 mM, optimal concentration for polymerase N1: 20 mM
Mg2+
-
DNA polymerase alpha: increasing concentrations of Mg2+ lead to a dramatically increased affinity for poly(dT) and poly(dC) polypyrimidines, has little or no effect on the interaction of the enzyme with poly(dA)
Mg2+
-
free Mg2+ competes with primer for enzyme binding, dramatic inhibition at Mg2+ concentration above the optimum, catalytic core binds primer through a Mg2+-chelate, with each of 4 Mg2+ ions acting to coordinate 2 phosphodiester groups
Mg2+
-
DNA polymerase lambda is not able to perform de novo DNA synthesis in the absence of a metal ion activator. Synthesis of de novo DNA is much stronger with Mn2+ than with Mg2+
Mg2+
-
peak activity in the presence of Mg2+ is observed in the range of 0.1-0.5 mM and is significantly reduced at concentrations above 2 mM
Mg2+
-
poly(dA)/oligo(dT)10:1. In the presence of Mn2+, DNA polymerase beta incorporates (biphenylcarbonyl)-4-oxobutyl triphosphate both on an intact template and opposite to an abasic site. DNA polymerase beta incorporates dCTP on the undamaged template, whereas it exclusively incorporates dATP opposite the abasic site. The incorporation efficiency of (biphenylcarbonyl)-4-oxobutyl triphosphate by DNA polymerase beta is 2fold higher in the presence of the undamaged template, with respect to the one carrying an abasic site. When Mn2+ is replaced by Mg2+, this difference becomes even more striking, so that (biphenylcarbonyl)-4-oxobutyl triphosphate can be exclusively incorporated on the undamaged in the presence of Mg2+, the incorporation of (biphenylcarbonyl)-4-oxobutyl triphosphate by DNA polymerase beta becomes strictly dependent on the presence of a templating base. Replacement of Mn2+ with Mg2+, however, greatly enhances the preference for incorporation of dCTP versus (biphenylcarbonyl)-4-oxobutyl triphosphate opposite a template G by DNA polymerase beta, which increases from 23fold to 239fold
Mg2+
-
pol zeta functions best in the presence of 1-5mM MgCl2, but exhibits dramatically lower activity in the presence of MnCl2
Mg2+
DNA polymerase iota contains two catalytic Mg2+ ions in the active site
Mg2+
strongly activated by the presence of Mg2+ at an optimum concentration of 3 mM
Mg2+
-
varying magnesium concentration affects both slippage and overall DNA synthesisof DNA polymerase PolB and PolD. There is almost no synthesis by PolB, PolD or their exo-forms at low magnesium concentrations (0.10.5 mM). Synthesis is also inhibited at 1520 mM. Parental molecules are readily detectable together with heteroduplex molecules at low to medium magnesium concentrations (15 mM)
Mg2+
the negative charge and the side-chain length of D259 might play a supporting role in coordinating the conserved Mg2+ to the correct position at the active center in the exonuclease domain
Mg2+
cofactor for both the polymerase and pyrophosphorolysis activities
Mg2+
DNA polymerase Dpo2 and Dpo3 are both more active with Mg2+ than Mn2+. DNA polymerase Dpo1 and Dpo4 are similarly active with Mg2+ or Mn2+
Mg2+
causes a concentration-dependent shift in the translocation equilibrium, predominantly by decreasing the forward translocation rate
Mg2+
-
exonuclease acitivity shows equal efficiency with Mg2+ and Mn2+, mutant D190A shows preference for Mn2+
Mg2+
-
higher polymerase activity with Mg2+ than with Mn2+, exonuclease acitivity shows equal efficiency with Mg2+ and Mn2+
Mg2+
the enzyme requires an extremely low concentration of Mg+2 cations for activity. A broad plateau is observed between 0.1 and 2 mM MgCl2. Concentrations above 2 mM are inhibitory. 20% of the activity of the plateau value is still observed even if no MgCl2 is added to the assay
Mg2+
PI-TfuI utilizes either Mg2+ or Mn2+, PI-TfuII only utilizes Mg2+
Mg2+
activity is dependent on a divalent cation, among which magnesium ion is optimal
Mg2+
requires a divalent cation, optimal activity is obtained with 2.0 mM MgSO4, recombinant enzyme with the nonspecific DNA-binding protein Sso7d from Sulfolobus solfataricus fused to the C-terminus
Mg2+
highly dependent on MgCl2 in the range of 0-20 mM with maximal activity at 14 mM MgCl2 and no detectable activity in the absence of MgCl2
Mg2+
-
highly dependent on MgCl2, with maximal activity at 12 mM MgCl2 and no detectable activity in the absence of MgCl2
Mg2+
-
highly dependent on MgCl2, with maximal activity at 14 mM MgCl2 and no detectable activity in the absence of MgCl2
Mg2+
no activity is detected in the absence of magnesium, activity is maximal between 1.5 and 3.0 mM MgCl2
Mg2+
-
optimal processivity at 6 mM, no synthesis is observed in the absence of Mg2+
Mn2+
divalent cation required. Maximum activity is observed with 6 mM MgCl2, whereas about 50% activity is obtained with MnCl2 at its optimal concentration of 6 mM
Mn2+
activates, Mn2+ shows a 8.6fold higher catalytic efficiency than Mg2+
Mn2+
-
the polymerase activity of PolX is strongly stimulated by Mn2+
Mn2+
activates. When Mg2+ is replaced with Mn2+, the efficiency of incorporation of dTMP opposite dA increases by 3fold
Mn2+
-
supports chemistry, but leads to markedly decreased fidelity by accelerating the rate of incorporation of mismatches, routinely used to generate random mutations during PCR. Mn2+ accommodates square planar, tetrahedral, and octahedral coordination
Mn2+
-
stimulates at 0.5-0.6 mM, 5fold more effective than optimal Mg2+ concentration
Mn2+
polI activity is absolutely dependent on the presence of divalent cations Mg2+ and Mn2+, Mn2+ cannot be replaced with Mg2+ completely
Mn2+
-
DNA polymerase lambda is not able to perform de novo DNA synthesis in the absence of a metal ion activator. Synthesis of de novo DNA is much stronger with Mn2+ than with Mg2+
Mn2+
-
DNA polymerase iota exhibits the greatest activity in the presence of low levels of Mn2+ (0.05-0.25 mM). Mn2+ increases the catalytic activity of DNA polymerase iota by about 30000-60000fold through a strong decrease in the Km value for nucleotide incorporation. Whereas DNA polymerase iota preferentially misinserts G opposite T by a factor of about 1.4-2.5fold over the correct base A in the presence of 0.25 and 5 mM Mg2+, respectively, the correct insertion of A is actually favored 2fold over the misincorporation of guanine in the presence of 0.075 mM Mn2+. Low levels of Mn2+ also dramatically increase the ability of DNA polymerase iota to traverse a variety of DNA lesions in vitro. The cation utilized by DNA polymerase iota in vivo may be Mn2+
Mn2+
-
incorporation of the NNTPs is observed only in the presence of its optimal activator, Mn2+
Mn2+
-
poly(dA)/oligo(dT)10:1. In the presence of Mn2+, DNA polymerase beta incorporates (biphenylcarbonyl)-4-oxobutyl triphosphate both on an intact template and opposite to an abasic site. DNA polymerase beta incorporates dCTP on the undamaged template, whereas it exclusively incorporates dATP opposite the abasic site. The incorporation efficiency of (biphenylcarbonyl)-4-oxobutyl triphosphate by DNA polymerase beta is 2fold higher in the presence of the undamaged template, with respect to the one carrying an abasic site. When Mn2+ is replaced by Mg2+, this difference becomes even more striking, so that (biphenylcarbonyl)-4-oxobutyl triphosphate can be exclusively incorporated on the undamaged in the presence of Mg2+, the incorporation of (biphenylcarbonyl)-4-oxobutyl triphosphate by DNA polymerase beta becomes strictly dependent on the presence of a templating base. Replacement of Mn2+ with Mg2+, however, greatly enhances the preference for incorporation of dCTP versus (biphenylcarbonyl)-4-oxobutyl triphosphate opposite a template G by DNA polymerase beta, which increases from 23fold to 239fold
Mn2+
-
pol iota displays its highest activity in the presence of MnCl2 at low concentrations of 0.05-0.1mM, its activity also peaks at low Mg2+, but is considerably higher in the presence of Mn2+
Mn2+
-
stimulates at 0.5 mM, about a third the maximal activity with Mg2+
Mn2+
in a MnCl2-soaked crystal, a Mn2+ is bound to one of the oxygens of the Asp111 side chain
Mn2+
DNA polymerase Dpo2 and Dpo3 are both more active with Mg2+ than Mn2+. DNA polymerase Dpo1 and Dpo4 are similarly active with Mg2+ or Mn2+
Mn2+
causes a concentration-dependent shift in the translocation equilibrium, predominantly by decreasing the forward translocation rate. Decreases the dNTP dissociation rate relative to Mg2+
Mn2+
-
exonuclease acitivity shows equal efficiency with Mg2+ and Mn2+, mutant D190A shows preference for Mn2+
Mn2+
PI-TfuI utilizes either Mg2+ or Mn2+, PI-TfuII only utilizes Mg2+
Mn2+
-
enzyme prefers Mn2+ over Mg2+ for RNase H activity, optimal concentration: 1.5-2.5 mM
Na+
-
pols beta, iota and zeta exhibit maximal activity under conditions of moderate NaCl concentrations of 20-60 mM
NaCl
optimum salt concentration is either 50 mM KCl or 75 mM NaCl
NaCl
in absence of NaCl, Tga PolB displays 67% polymerization activity. From 50 to 200 mM NaCl, the activity is higher than 90%, but it is significantly reduced at NaCl concentrations above 400 mM
Zn2+
-
10-13% of the activity with Mg2+, optimal concentration: 0.3-0.5 mM
Zn2+
-
required, Zn2+ is bound to the CysA motif in yeast B family DNA polymerases
additional information
no activation by Fe2+, Ca2+, Zn2+, Cd2+, Sr2+, Ba2+, Cu2+, and Cr3+. Ca2+ concentration required to obtain the half-maximal incorporation rate under single-turnover conditions was 0.63 mM
additional information
-
no activation by Fe2+, Ca2+, Zn2+, Cd2+, Sr2+, Ba2+, Cu2+, and Cr3+. Ca2+ concentration required to obtain the half-maximal incorporation rate under single-turnover conditions was 0.63 mM
additional information
-
Ca2+ supports nucleotide binding but not catalysis
additional information
polI activity requires the presence of monovalent ions, above 100 mM, monovalent salts become inhibitory for the activity
additional information
-
DNA binding, dNTP binding and catalytic activity of mutant enzyme in the presence of two metal ions, Mg2+ and Mn2+, overview. Amino acid residues D378 and D531 are mainly responsible for the binding of metal chelated substrate dNTP
additional information
-
the PolX catalytic domain exhibits no polymerase activity with 5 mM Zn2+, Ni2+, Ca2+ or Co2+, or without a metal ion
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
(2E)-2-(3-nitro-4-[[6-(trifluoromethyl)pyridin-3-yl]sulfanyl]benzylidene)-5-thioxo-1,3-thiazolidin-4-one
-
-
(2E)-2-[4-(2-hydroxyethyl)-3-nitrobenzylidene]-5-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[3-bromo-4-[(4-fluorobenzyl)oxy]benzylidene]-1,3-thiazolidine-2,4-dione
-
-
(5Z)-5-[3-bromo-4-[(4-fluorophenyl)sulfanyl]benzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[3-nitro-4-(pyridin-3-ylsulfanyl)benzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[4-(4-methylphenoxy)-3-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[4-(cyclohexylsulfanyl)-3-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[4-[(4-bromophenyl)sulfanyl]-3-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[4-[(4-chlorophenyl)sulfanyl]-3-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[4-[(4-fluorobenzyl)oxy]-3-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[4-[(4-methylphenyl)sulfanyl]-3-nitrobenzylidene]-3-(prop-2-en-1-yl)-2-thioxo-1,3-thiazolidin-4-one
-
-
(9-adenylmethylcarbonyl)-4-aminobutyl triphosphate
-
fully competitive with respect to the nucleotide substrate dTTP, inhibits wild-type enzyme and mutant enzyme Y505A
(biphenylcarbonyl)-4-oxobutyl triphosphate
-
fully competitive with respect to the nucleotide substrate dTTP, inhibits wild-type enzyme and mutant enzyme Y505A; inhibits wild-type enzyme and mutant enzyme Y505A
(NH4)2SO4
-
optimal concentration of 20 mM, inhibition below and above 20 mM
1,2,3,4-tetrahydro-5-methoxynaphthalene-1,4-diol
-
i.e. nodulisporol. Strong inhibition of pol lambda, but does not influence the activities of mammalian pols alpha to kappa, and shows no effect on the activities of plant pols alpha and beta, prokaryotic pols, and other DNA metabolic enzymes such as calf terminal deoxynucleotidyl transferase, human immunodeficiency virus type-1 (HIV-1) reverse transcriptase, human telomerase, T7 RNA polymerase, and bovine deoxyribonuclease I
2-(4-azidophenacyl)thio-2'-deoxyadenosine 5'-triphosphate
-
template-competitive DNA polymerase inhibitor
-
2-methoxy-4-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl 2,4-dichlorobenzoate
-
-
2-methoxy-4-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl 3-bromobenzoate
-
-
2-thiomethyl-6-phenyl-4-(4'-hydroxybutyl)-1,2,4,-triazole (5,1-C)(1,2,4)triazine-7-one triphosphate
-
fully competitive with respect to the nucleotide substrate dTTP; fully competitive with respect to the nucleotide substrate dTTP, inhibits wild-type enzyme and mutant enzyme Y505A
3'-azido-2',3'-dideoxythymidine 5'-phosphate
-
50% inhibition at 0.22 mM
3,4-dihydro-4-hydroxy-8-methoxynaphthalen-1(2H)-one
-
i.e. nodulisporone. Strong inhibition of pol lambda, but does not influence the activities of mammalian pols alpha to kappa, and shows no effect on the activities of plant pols alpha and beta, prokaryotic pols, and other DNA metabolic enzymes such as calf terminal deoxynucleotidyl transferase, human immunodeficiency virus type-1 (HIV-1) reverse transcriptase, human telomerase, T7 RNA polymerase, and bovine deoxyribonuclease I
3-(2'-deoxy-beta-D-erythro-pentofuranosyl) pyrimido[1,2-alpha]purin-10(3H)-one
-
i.e. M1dG. When paired opposite cytosine in duplex DNA at physiological pH,M1dG undergoes ring opening to form N2-(3-oxo-1-propenyl)-dG. To improve the understanding of the basis for M1dG-induced mutagenesis, the mechanism of translesion DNA synthesis opposite M1dG by the model Y-family polymerase Dpo4 is studied at a molecular level using kinetic and structural approaches. Steady-state and transient-state kinetic results both indicate that Dpo4 catalysis is inhibited by M1dG (260-2900-fold), with dATP being the favored insertion event for both sequences tested
4-oxo-dihydroquinoline
-
binds at the polymerase active site interacting non-covalently with both the polymerase and the DNA duplex
4-[(Z)-(2,4-dioxo-1,3-thiazolidin-5-ylidene)methyl]-2-methoxyphenyl 3-bromobenzoate
-
-
4-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl 2-chlorobenzoate
-
-
5-(5-nitro-2-[[6-(trifluoromethyl)pyridin-3-yl]sulfanyl]benzylidene)-2-thioxo-1,3-thiazolidin-4-one
-
-
5-[2-(cyclohexylsulfanyl)-5-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
5-[2-[(4-chlorophenyl)sulfanyl]-5-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
5-[2-[(4-methylphenyl)sulfanyl]-5-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
6-chloro-1,4-dihydro-4-oxo-1-(beta-D-ribofuranosyl) quinoline-3-carboxylic acid
-
noncompetitive inhibitor
alpha-(4-azidophenyl)-1,N6-etheno-dATP
-
template-competitive DNA polymerase inhibitor
ammonium-21-tungsto-9-antimoniate
-
HPA-23, antiviral drug, noncompetitive to TTP, activated DNA, poly(rA)-oligo(dT), wheat germ DNA polymerase A, a gamma-like DNA polymerase
-
aptamer
-
nucleotide ligands of small size and unique three-dimensional structure, TQ21 family, presence of loop is necessary for inhibition
-
aurintricarboxylic acid
-
potent nanomolar inhibitor of pol beta, pol iota, and pol zeta
cis-syn thymine dimer
Dpo4 is severely blocked by the presence of a cis-syn thymine dimer in the template
cloretazine
-
i.e. 1,2-bis[methylsulfonyl]-1-[2-chloroethyl]-2-[(methylamino)carbonyl]hydrazine
dATP
-
using dATP as an inhibitor and dCTP as a varied substrate, the pattern of inhibition is competitive
deoxynucleoside triphosphate
-
work as competitive inhibitors depending on their incorporation sites, A-incorporation is strongly inhibited by dTTP and dGTP, T-incorporation is inhibited by dATP, G-and C-incorporation sites are less sensitive to competitive inhibition
gemcitabine
-
i.e. 2'-deoxy-2',2'-difluorocytidine, when gemcitabine is encountered as a template base DNA polymerase gamma pauses at the lesion and one downstream position but eventually elongates the primer to full-length product, these pauses are because of a 1000fold decrease in nucleotide incorporation efficiency
hymenoic acid
-
specific inhibitor of human DNA polymerase lambda, non-competitive inhibition with respect to both the DNA template-primer and the dNTP, i.e trans-4-[(1'E,5'S)-5'-carboxy-1'-methyl-1'-hexenyl]cyclohexanecarboxylic acid, does not influence the activities of the other mammalian pols alpha, gamma, delta, epsilon, eta, iota, and kappa, and also shows no effect even on the activity of pol beta
hypoxanthine
-
traces of uracil and hypoxanthine in DNA can lead to inhibition of the polymerase chain reaction by archaeal DNA polymerases
N-(2,4-dinitro-5-fluorophenyl)-2-aminoethyl triphosphate
-
inhibition of mutant enzyme Y505A, inactive against wild-type enzyme
N-(2,4-dinitro-5-fluorophenyl)-4-aminobutyl triphosphate
-
fully competitive with respect to the nucleotide substrate dTTP, inhibits wild-type enzyme and mutant enzyme Y505A
N-(2,4-dinitro-5-imidazolylphenyl)-2-aminoethyl triphosphate
-
inhibition of mutant enzyme Y505A, inactive against wild-type enzyme
N-(2,4-dinitro-5-imidazolylphenyl)-4-aminobutyl triphosphate
-
inhibition of mutant enzyme Y505A, inactive against wild-type enzyme
N-(2,4-dinitrophenyl)-4-aminobutyl triphosphate
-
fully competitive with respect to the nucleotide substrate dTTP, inhibits wild-type enzyme and mutant enzyme Y505A
N-(benzyloxycarbonyl)-4-aminobutyl triphosphate
-
fully competitive with respect to the nucleotide substrate dTTP, inhibits wild-type enzyme and mutant enzyme Y505A; inhibits wild-type enzyme and mutant enzyme Y505A
N-[6-N-(2,4-dinitrophenyl)aminohexanoyl]-2-aminoethyl triphosphate
-
inhibition of mutant enzyme Y505A, inactive against wild-type enzyme
N2,N2-dimethyl guanine
the presence of N2,N2-dimethyl guanine lowers the catalytic efficiency for incorporation of dCTP of DNA polymerase Dpo4 16000fold
N2,N2-dimethylguanine
the presence of N2,N2-dimethylguanine lowers the catalytic efficiency of the DNA polymerase Dpo4 16000fold. Dpo4 inserts dNTPs almost at random during bypass of N2,N2-dimethylguanine, and much of the enzyme is kinetically trapped by an inactive ternary complex when N2,N2-dimethylguanine is present
N2-CH2(9-anthracenyl)guanine
-
severely blocks activity, frequencies of dATP misinsertion and extension beyond mispairs are proportionally increased, great decrease in pre-steady-state kinetic burst rate. 2.6fold decrease in dCTP binding affinity and increased DNA substrate binding affinity
neobavaisoflavone
-
isolated from Psoralea corylifolia, inhibition at moderate to high concentrations
NSC-666715
potent, small molecular weight inhibitor of DNA polymerase beta, blocks Pol-beta-directed single-nucleotide- and long-patch-base excisison repair
RecA
-
exonuclease activity of pol II can be inhibited by the presence of RecA protein and single-strand binding protein
-
Replication factor C
DNA polymerization by Dpo2 and Dpo3 is strongly inhibited; DNA polymerization by Dpo2 and Dpo3 is strongly inhibited
-
rhodanines
-
most potent inhibitors for DNA Pol lambda, they are up to 10times less active against the highly similar DNA polymerase beta, structure-activity relationships, overview. 5-Arylidene-2,4-thiazolidinediones are class I rhodanines, rhodanine class II has members of carbohydrazides, and class III contains a common 2,4-pentadione substructure element
-
single-stranded binding protein
DNA polymerization by Dpo2 and Dpo3 is strongly inhibited; DNA polymerization by Dpo2 and Dpo3 is strongly inhibited; DNA synthesis by DNA polymerase Dpo2 and Dpo3 is remarkably decreased by single-stranded binding protein; DNA synthesis by DNA polymerase Dpo2 and Dpo3 is remarkably decreased by single-stranded binding protein
-
SsoCdc6-2 protein
-
inhibits both the DNA-binding activity and DNA polymerization activity of SsoPolY on the DNA substrates containing mismatched bases, while it forms a large complex with SsoPolY and stimulates DNA-binding activity on paired primer-template DNA substrates
-
sulfoglycolipid beta-sulfoquinovosyldiacylglycerol
-
inhibits the DNA polymerase activity of pol lambda by binding to the Met1-Arg95 region and inhibiting its nuclear transit
-
sulfoquinovosyl diacylglycerol
-
significant inhibition of activity at 0.1 mg/ml in strain JM109, but not in strains TOP10, TOP10F, or DH5alpha
Uracil
-
traces of uracil and hypoxanthine in DNA can lead to inhibition of the polymerase chain reaction by archaeal DNA polymerases
vitamin K3
-
more than 80% inhibition of pol gamma at 0.03 mM, does not affect other human DNA polymerase isozymes
[3-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenoxy]acetic acid
-
-
1-deoxyrubralactone
-
potent inhibitor of isozymes pol kappa, pol lambda, pol iota, and pol eta, but does not inhibit DNA polymerase isozymes pol delta, pol epsilon, and pol gamma
2',3'-dideoxyribosylthymine triphosphate
-
17% and 33% inhibition are observed with ddTTP/dTTP ratios of 1:1 and 5:1, respectively
2',3'-dideoxyribosylthymine triphosphate
-
the enzyme is slightly sensitive to. 25% inhibition is observed with a ddTTP/dTTP ratio of 50
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
inhibition of DNA polymerase alpha
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
inhibition of DNA polymerase alpha at 100fold lower concentration than DNA polymerase delta
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
polymerase delta and epsilon
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
DNA polymerase alpha
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
inhibition of DNA polymerase alpha at 100fold lower concentration than DNA polymerase delta
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
inhibition of DNA polymerase alpha at 100fold lower concentration than DNA polymerase delta
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
inhibition of DNA polymerase alpha at 100fold lower concentration than DNA polymerase delta
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
inhibition of DNA polymerase alpha at 100fold lower concentration than DNA polymerase delta
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
phage T4 enzyme inhibited with lower sensitivity than other members of the B family DNA polymerases
aphidicolin
-
DNA polymerase alpha; DNA polymerase delta; DNA polymerase epsilon
aphidicolin
-
DNA polymerase alpha; DNA polymerase delta; DNA polymerase epsilon
aphidicolin
-
DNA polymerase alpha; DNA polymerase delta; DNA polymerase epsilon
aphidicolin
-
DNA polymerase alpha; DNA polymerase delta; DNA polymerase epsilon
aphidicolin
-
inhibition is competitive for dCTP, noncompetitive for dATP, dGTP and dTTP and uncompetitive for activated DNA
aphidicolin
-
DNA polymerase alpha; DNA polymerase delta; DNA polymerase epsilon
aphidicolin
-
DNA polymerase alpha; DNA polymerase delta; DNA polymerase epsilon
aphidicolin
-
phage T4 enzyme inhibited with lower sensitivity than other members of the B family DNA polymerases
aphidicolin
-
DNA polymerase alpha; DNA polymerase delta; DNA polymerase epsilon
Carbonyldiphosphonate
-
DNA polymerase delta; no inhibition of polymerase alpha
Carbonyldiphosphonate
-
DNA polymerase delta; no inhibition of polymerase alpha
Carbonyldiphosphonate
-
DNA polymerase delta; no inhibition of polymerase alpha
ddTTP
-
processivity is strongly inhibited in the presence of 0.01 and 0.02 mM ddTTP
Dideoxynucleoside 5'-triphosphate
-
polymerase epsilon, slightly sensitive
dimethyl sulfoxide
-
inhibition of DNA polymerase epsilon, stimulation of DNA polymerase delta
dimethyl sulfoxide
-
stimulates DNA polymerase alpha and delta, inhibits human DNA polymerase epsilon
diphosphate
-
analogs, phage T4 enzyme inhibited with lower sensitivity than other members of the B family DNA polymerases
Halenaquinol sulfate
-
potential inhibitor of DNA polymerase alpha and epsilon, less effective against Escherichia coli DNA polymerase
Halenaquinol sulfate
-
potential inhibitor of DNA polymerase alpha and epsilon, less effective against Escherichia coli DNA polymerase
lysophosphatidic acid
-
isolated from myxamoebae of Physarum polycephalum, 90% inhibition of polymerase alpha, weak inhibitor of polymerase beta
Mg2+
-
DNA polymerase alpha: free Mg2+ competes with primer for enzyme binding, dramatic inhibition at Mg2+ concentration above the optimum
Mg2+
-
DNA polymerase alpha: free Mg2+ competes with primer for enzyme binding, dramatic inhibition at Mg2+ concentration above the optimum
Mg2+
-
required, substrate-like inhibition by Mg2+ occur, the inhibition is not due to enzyme inactivation, but instead due to the decrease in rate of a step after chemistry
Mn2+
-
inhibits 3'-5'-proofreading activity, thereby decreasing the fidelity of DNA replication by 50%
N-ethylmaleimide
-
great sensitivity of phage-induced enzyme, relative insensitivity of pol I
N-ethylmaleimide
-
69-96% inhibition at 0.0007 mM, 46-54% inhibition at 0.007 mM
N-ethylmaleimide
-
great sensitivity of phage-induced enzyme, relative insensitivity of pol I
N-ethylmaleimide
-
great sensitivity of phage-induced enzyme, relative insensitivity of pol I
N-ethylmaleimide
-
inhibited when preincubation with this reagent is performed at 65°C
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
inhibition of DNA polymerase alpha
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
inhibition of DNA polymerase alpha at 100fold; lower concentration than DNA polymerase delta
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
100-fold, polymerase delta and epsilon
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
inhibition at 0.1 mM
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
inhibition of DNA polymerase alpha at 100fold; lower concentration than DNA polymerase delta
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
inhibition of DNA polymerase alpha at 100fold; lower concentration than DNA polymerase delta
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
inhibition of DNA polymerase alpha at 100fold; lower concentration than DNA polymerase delta
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
inhibition of DNA polymerase alpha at 100fold; lower concentration than DNA polymerase delta
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
alpha-like enzyme relatively resistant
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
50% inhibition at 0.08 mg/ml
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
mechanism depends upon assay conditions, reversible competitive inhibition predominates
NaCl
in absence of NaCl, Tga PolB displays 67% polymerization activity. From 50 to 200 mM NaCl, the activity is higher than 90%, but it is significantly reduced at NaCl concentrations above 400 mM
poly(rA)-p(dT)45
-
inhibitory effect towards the reverse transcriptase activity of K4polL329A
-
poly(rA)-p(dT)45
inhibitory effect towards the reverse transcriptase activity of M1pol
-
Salt
-
optimal activity in presence of total salt concentration of approximately 0.1 M, 97% inhibition at 0.3 M
single-stranded DNA
-
inhibition of polymerase alpha, competitive with respect to activated DNA substrate
single-stranded DNA
-
inhibition of polymerase alpha, competitive with respect to activated DNA substrate
additional information
-
Pol X is not inhibited noticeably by up to 1 mM diphosphate, at higher concentrations there is modest inhibition
-
additional information
-
no inhibition of DNA polymerase epsilon by 2-(p-n-butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
additional information
-
no inhibition by dideoxynucleoside 5'-triphosphate; no inhibition of DNA polymerase beta and gamma by aphidicolin; no inhibition of DNA polymerase beta by N-ethylmaleimide; no inhibition of DNA polymerase beta, gamma, delta, epsilon by 2-(p-n-butylanilino)-2'-deoxyadenosine 5'-triphosphate; no inhibition of polymerase alpha and delta by dideoxynucleoside 5'-triphosphate
-
additional information
-
inhibitor analysis of calf thymus DNA polymerase alpha, delta and epsilon
-
additional information
-
DNA polymerase alpha is not inhibited by vitamin K1, vitamin K2, and vitamin K3
-
additional information
-
DNA polymerase alpha is not inhibited by allicin, alliin, diallyl trisulfide, diallyl tetrasulfide, and diallyl pentasulfide
-
additional information
-
not inhibited by 1-deoxyrubralactone and talaroflavone
-
additional information
-
DNA polymerase isozymes I and II are not inhibited by diallyl trisulfide, diallyl tetrasulfide, and diallyl pentasulfide
-
additional information
-
no inhibition by aphidicolin; no inhibition by ara-CTP
-
additional information
-
no inhibition by dideoxynucleoside 5'-triphosphate; no inhibition of DNA polymerase beta and gamma by aphidicolin; no inhibition of DNA polymerase beta by N-ethylmaleimide; no inhibition of DNA polymerase beta, gamma, delta, epsilon by 2-(p-n-butylanilino)-2'-deoxyadenosine 5'-triphosphate; no inhibition of polymerase alpha and delta by dideoxynucleoside 5'-triphosphate
-
additional information
-
enzyme is resistant to NEM and 2',3'-dideoxythymidine 5-triphosphate
-
additional information
-
DNA polymerase isozymes alpha, delta and epsilon are not inhibited by diallyl trisulfide, diallyl tetrasulfide, and diallyl pentasulfide
-
additional information
-
no inhibition of DNA polymerase beta or gamma from various eukaryotic species, DNA polymerase I from E. coli by lysophosphatidic acid
-
additional information
-
not inhibited by 1-deoxyrubralactone and talaroflavone
-
additional information
-
DNA polymerase I is not inhibited by diallyl trisulfide, diallyl tetrasulfide, and diallyl pentasulfide
-
additional information
-
monogalactosyl diacylglycerol and digalactosyl diacylglycerol do not have any inhibitory effect on enzymatic activity
-
additional information
-
no inhibition by dideoxynucleoside 5'-triphosphate; no inhibition of DNA polymerase beta and gamma by aphidicolin; no inhibition of DNA polymerase beta by N-ethylmaleimide; no inhibition of DNA polymerase beta, gamma, delta, epsilon by 2-(p-n-butylanilino)-2'-deoxyadenosine 5'-triphosphate; no inhibition of polymerase alpha and delta by dideoxynucleoside 5'-triphosphate
-
additional information
polI activity requires the presence of monovalent ions, above 100 mM, monovalent salts become inhibitory for the activity
-
additional information
-
no inhibition by dideoxynucleoside 5'-triphosphate; no inhibition of DNA polymerase beta and gamma by aphidicolin; no inhibition of DNA polymerase beta by N-ethylmaleimide; no inhibition of DNA polymerase beta, gamma, delta, epsilon by 2-(p-n-butylanilino)-2'-deoxyadenosine 5'-triphosphate; no inhibition of polymerase alpha and delta by dideoxynucleoside 5'-triphosphate
-
additional information
-
no inhibition by (9-adenylmethylcarbonyl)-4-aminobutyl, N-(2,4-dinitrophenyl)-4-aminobutyl triphosphate, N-(2,4-dinitro-5-fluorophenyl)-4-aminobutyl triphosphate, N-[6-N-(2,4-dinitrophenyl)aminohexanoyl]-2-aminoethyl triphosphate, N-(2,4-dinitro-5-fluorophenyl)-2-aminoethyl triphosphate, N-(2,4-dinitro-5-imidazolylphenyl)-4-aminobutyl triphosphate and N-(2,4-dinitro-5-imidazolylphenyl)-2-aminoethyl triphosphate
-
additional information
-
DNA polymerase isozymes are not inhibited by vitamin K1 and vitamin K2
-
additional information
-
DNA polymerase lambda is strongly inhibited by an extract from Allium sativum consisting of diallyl trisulfide, diallyl tetrasulfide, and diallyl pentasulfide, competitive inhibitor
-
additional information
-
isozyme DNA polymerase lambda is not inhibited by mucocin
-
additional information
-
no inhibition by 2',3'-dideoxythymidine 5'-triphosphate; no inhibition by aphidicolin; no inhibition by ara-CTP
-
additional information
-
no inhibition by dideoxynucleoside 5'-triphosphate; no inhibition of DNA polymerase beta and gamma by aphidicolin; no inhibition of DNA polymerase beta by N-ethylmaleimide; no inhibition of DNA polymerase beta, gamma, delta, epsilon by 2-(p-n-butylanilino)-2'-deoxyadenosine 5'-triphosphate; no inhibition of polymerase alpha and delta by dideoxynucleoside 5'-triphosphate
-
additional information
-
no inhibition of DNA polymerase beta or gamma from various eukaryotic species, DNA polymerase I from E. coli by lysophosphatidic acid
-
additional information
-
DNA polymerase delta is not inhibited by diallyl trisulfide, diallyl tetrasulfide, and diallyl pentasulfide
-
additional information
no inhibition by 0.1 mM aphidicolin
-
additional information
DNA polymerizing activity is not inhibited by aphidicolin at concentrations up to 2 mM that inhibit the activities of Pfu Pol I and other alpha-like DNA polymerases.
-
additional information
-
DNA polymerizing activity is not inhibited by aphidicolin at concentrations up to 2 mM that inhibit the activities of Pfu Pol I and other alpha-like DNA polymerases.
-
additional information
-
DNA polymerase beta is not inhibited by vitamin K1, vitamin K2, and vitamin K3
-
additional information
-
DNA polymerase beta is strongly inhibited by an extract from Allium sativum consisting of diallyl trisulfide, diallyl tetrasulfide, and diallyl pentasulfide, competitive inhibitor
-
additional information
-
not inhibited by gamma-lactone, mucocin, jimenezin, and 19-epi-jimenezin
-
additional information
-
reverse gyrase inhibits DNA polymerase PolB1. Inhibition of PolY activity depends on both ATPase and topoisomerase activities of reverse gyrase, suggesting that the intact positive supercoiling activity is required for PolY inhibition. In vivo, reverse gyrase and PolY are degraded after induction of DNA damage. Inhibition by reverse gyrase and degradation might act as a double mechanism to control DNA polymerase PolY and prevent its potentially mutagenic activity when undesired. Inhibition of a translesion polymerase by topoisomerase-induced modification of DNA structure may represent a mechanism of regulation of these enzymes
-
additional information
-
the enzyme is resistant to 0.02 mg/ml aphidicolin
-
additional information
no inhibition by 0.02 mg/ml aphidicolin. The enzyme is inhibited by dideoxy- and arabinosine-analogs and SH-blocking agents
-
additional information
-
inhibitor analysis of bacteriophage T4 DNA polymerase
-
additional information
-
not inhibited by 1-deoxyrubralactone and talaroflavone
-
additional information
-
DNA polymerase is not inhibited by diallyl trisulfide, diallyl tetrasulfide, and diallyl pentasulfide
-
additional information
PI-TfuII is inhibited by one of the cleavage products
-
additional information
-
high concentrations of DNA-primed RNA template decrease the efficiency of cDNA synthesis with bacterial family A DNA polymerases
-
additional information
-
not inhibited by 1-deoxyrubralactone and talaroflavone
-
additional information
-
DNA polymerase is not inhibited by diallyl trisulfide, diallyl tetrasulfide, and diallyl pentasulfide
-
additional information
high concentrations of DNA-primed RNA template decrease the efficiency of cDNA synthesis with bacterial family A DNA polymerases
-
additional information
-
enzyme is not inhibited by cytosine-beta-D-arabinofuranoside 5'-triphosphate which is an inhibitor of alpha-polymerase, monoclonal antibodies against human DNA polymerase alpha do not bind; no inhibition by aphidicolin
-
additional information
-
no inhibition by dideoxynucleoside 5'-triphosphate; no inhibition of DNA polymerase beta and gamma by aphidicolin; no inhibition of DNA polymerase beta by N-ethylmaleimide; no inhibition of DNA polymerase beta, gamma, delta, epsilon by 2-(p-n-butylanilino)-2'-deoxyadenosine 5'-triphosphate; no inhibition of polymerase alpha and delta by dideoxynucleoside 5'-triphosphate
-
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
(NH4)2SO4
-
optimal concentration of 20 mM, inhibition below and above 20 mM
Aeropyrum pernix proliferating cell nuclear antigen 1
three genes encoding proliferating cell nuclear antigen (PCNA)-like sequences are identified in the genome of Aeropyrum pernix. The genes are cloned and expressed in Escherichia coli and the gene products are analyzed. All three proliferating cell nuclear antigen homologs stimulate the primer extension activities of the two DNA polymerases, polymerase I (Pol I) and Pol II in Aeropyrum pernix to various extents. Aeropyrum pernix PCNA 3 (ApePCNA3) provides a most remarkable effect on both Pol I and Pol II
-
Aeropyrum pernix proliferating cell nuclear antigen 3
three genes encoding proliferating cell nuclear antigen (PCNA)-like sequences are identified in the genome of Aeropyrum pernix. The genes are cloned and expressed in Escherichia coli and the gene products are analyzed. All three proliferating cell nuclear antigen homologs stimulate the primer extension activities of the two DNA polymerases, polymerase I (Pol I) and Pol II in Aeropyrum pernix to various extents. Aeropyrum pernix PCNA 3 (ApePCNA3) provides a most remarkable effect on both Pol I and Pol II
-
Auxiliary subunits
-
pol III can repair short gaps created by nuclease in duplex DNA, for efficient replication of the long, single-stranded templates pol III requires auxiliary subunits beta, gamma and delta
-
bovine serum albumin
DNA polymerase is stabilized with an approximately 25% increase in enzyme activity
-
FEN1
-
stimulates strand displacement activity, DEN1 processes nicked DNA, thus removing a barrier to Pol lambda DNA synthesis. It results in a one-nucleotide gapped DNA molecule that is a favorite substrate of Pol lambda
-
Methanosarcina acetivorans proliferating cell nuclear antigen
stimulates translesion DNA synthesis
-
pORF18
-
stimulates DNA polymerase activity of pORF30. pORF30 physically interacts with pORF18 through both a C-proximal region and the extreme C terminus
-
RecA
-
DNA polymerase V is activated by a RecA nucleoprotein filament, RecA transfers a single RecA-ATP stoichiometrically from its DNA 3'-end to free pol V (UmuD'2C) to form an active mutasome with the composition UmuD'2C-RecA-ATP
-
single-stranded-binding protein
-
SSB protein, Pol V has intrinsically weak DNA polymerase activity, but its catalytic activity can be stimulated in vitro in the presence the beta-processivity clamp, RecA protein bound to ssDNA, and single-stranded-binding protein
-
SsoCdc6
-
Orc1/Cdc6 proteins stimulate the DNA-binding ability of SsoPolB1 and differentially regulate both its polymerase and nuclease activities
-
Triton X-100
DNA polymerase is stabilized with an approximately 25% increase in enzyme activity
dimethyl sulfoxide
-
inhibition of DNA polymerase epsilon, stimulation of DNA polymerase delta
dimethyl sulfoxide
-
stimulates DNA polymerase alpha and delta, inhibits human DNA polymerase epsilon
dimethyl sulfoxide
-
stimulates DNA polymerase alpha and delta, inhibits human DNA polymerase epsilon
dimethyl sulfoxide
-
stimulates DNA polymerase alpha and delta, inhibits human DNA polymerase epsilon
dimethyl sulfoxide
-
stimulates DNA polymerase alpha and delta, inhibits human DNA polymerase epsilon
dimethyl sulfoxide
-
stimulates DNA polymerase alpha and delta, inhibits human DNA polymerase epsilon
Polyethylene glycol
-
410% of PEG 4000 or PEG 8000 can enhance the activity
Polyethylene glycol
-
410% of PEG 4000 or PEG 8000 can enhance the activity
proliferating cell nuclear antigen
-
interaction with monoubiquitylated proliferating cell nuclear antigen is necessary for biological activity and is required for translesion synthesis past UV photoproducts by Poleta
-
proliferating cell nuclear antigen
-
PCNA, specific auxiliary factor stimulating DNA polymerase delta
-
proliferating cell nuclear antigen
-
PCNA, specific auxiliary factor stimulating DNA polymerase delta
-
proliferating cell nuclear antigen
-
PCNA, specific auxiliary factor stimulating DNA polymerase delta
-
proliferating cell nuclear antigen
-
PCNA, specific auxiliary factor stimulating DNA polymerase delta
-
proliferating cell nuclear antigen
-
PCNA, Pol delta requires the DNA sliding clamp for highly processive enzyme activity. Pol delta interacts with proliferating cell nuclear antigen, PCNA, through multiple interactions
-
proliferating cell nuclear antigen
-
PCNA, the interaction between pol delta and PCNA is mediated predominantly by the p50 accessory subunit of pol delta and not the p125 catalytic subunit
-
proliferating cell nuclear antigen
-
PCNA, specific auxiliary factor stimulating DNA polymerase delta
-
proliferating cell nuclear antigen
-
PCNA, specific auxiliary factor stimulating DNA polymerase delta
-
proliferating cell nuclear antigen
-
PCNA, specific auxiliary factor stimulating DNA polymerase delta
-
proliferating cell nuclear antigen
-
is greatly enhanced by the presence of proliferating cell nuclear antigen and replication factor C
-
proliferating cell nuclear antigen
DNA synthesis by any of the DNA polymerases alone is not very processive. The addition of proliferating cell nuclear antigen slightly increases primer extension only by DNA polymerase Dpo4 but not by DNA polymerase Dpo1, Dpo2, or Dpo3. Both proliferating cell nuclear antigen and replication factor C enhance primer extension substantially in the cases of DNA polymerase Dpo1, Dpo3, and Dpo4 (which generate much longer extension products up to about 150-, 65-, and 150-mers, respectively) but very weakly with DNA polymerase Dpo2, which generates slightly more products of similar length up to about 80-mers. The addition of proliferating cell nuclear antigen, replication factor C, and single-stranded binding protein strongly increases DNA polymerization by Dpo1 and Dpo4, which yields extended products, mainly up to about 500-mers and 300-mers, respectively. An increase of the processivity of DNA synthesis in the presence of all accessory replication factors is the most prominent with Dpo1 and also with Dpo4
-
proliferating cell nuclear antigen
-
PCNA, specific auxiliary factor stimulating DNA polymerase delta
-
Replication factor A
-
RF-A, multisubunit single-stranded DNA-binding protein, functions as an auxiliary protein for both polymerases alpha and delta, required for initiation and elongation stages of in vitro SV40 DNA replication
-
Replication factor A
-
RF-A, multisubunit single-stranded DNA-binding protein, functions as an auxiliary protein for both polymerases alpha and delta, required for initiation and elongation stages of in vitro SV40 DNA replication
-
Replication factor A
-
RF-A, multisubunit single-stranded DNA-binding protein, functions as an auxiliary protein for both polymerases alpha and delta, required for initiation and elongation stages of in vitro SV40 DNA replication
-
Replication factor A
-
RF-A, multisubunit single-stranded DNA-binding protein, functions as an auxiliary protein for both polymerases alpha and delta, required for initiation and elongation stages of in vitro SV40 DNA replication
-
Replication factor A
-
RF-A, multisubunit single-stranded DNA-binding protein, functions as an auxiliary protein for both polymerases alpha and delta, required for initiation and elongation stages of in vitro SV40 DNA replication
-
Replication factor A
-
RF-A, multisubunit single-stranded DNA-binding protein, functions as an auxiliary protein for both polymerases alpha and delta, required for initiation and elongation stages of in vitro SV40 DNA replication
-
Replication factor C
-
RF-C, multisubunit protein complex with primer/template binding and DNA-dependent ATPase activity, has a profound effect on leading-strand DNA synthesis
-
Replication factor C
-
RF-C, multisubunit protein complex with primer/template binding and DNA-dependent ATPase activity, has a profound effect on leading-strand DNA synthesis
-
Replication factor C
-
RF-C, multisubunit protein complex with primer/template binding and DNA-dependent ATPase activity, has a profound effect on leading-strand DNA synthesis
-
Replication factor C
-
RF-C, multisubunit protein complex with primer/template binding and DNA-dependent ATPase activity, has a profound effect on leading-strand DNA synthesis
-
Replication factor C
-
RF-C, multisubunit protein complex with primer/template binding and DNA-dependent ATPase activity, has a profound effect on leading-strand DNA synthesis
-
Replication factor C
-
is greatly enhanced by the presence of proliferating cell nuclear antigen and replication factor C
-
Replication factor C
both proliferating cell nuclear antigen and replication factor C enhance primer extension substantially in the cases of DNA polymerase Dpo1, Dpo3, and Dpo4 (which generate much longer extension products up to about 150-, 65-, and 150-mers, respectively) but very weakly with DNA polymerase Dpo2, which generates slightly more products of similar length up to about 80-mers. The addition of proliferating cell nuclear antigen, replication factor C, and single-stranded binding protein strongly increases DNA polymerization by Dpo1 and Dpo4, which yields extended products, mainly up to about 500-mers and 300-mers, respectively. An increase of the processivity of DNA synthesis in the presence of all accessory replication factors (proliferating cell nuclear antigen, replication factor C, and single-stranded binding protein) is the most prominent with Dpo1 and also with Dpo4
-
Replication factor C
-
enhances both the polymerase and 3'-5' exonuclease activities of PolB1 in an ATP-independent manner
-
Replication factor C
-
RF-C, multisubunit protein complex with primer/template binding and DNA-dependent ATPase activity, has a profound effect on leading-strand DNA synthesis
-
single-stranded binding protein
an increase of the processivity of DNA synthesis in the presence of all accessory replication factors (proliferating cell nuclear antigen, replication factor C, and single-stranded binding protein) is the most prominent with Dpo1 and also with Dpo4 as compared with DNA polymerase Dpo2 and Dpo3
-
single-stranded binding protein
an increase of the processivity of DNA synthesis in the presence of all accessory replication factors (proliferating cell nuclear antigen, replication factor C, and single-stranded binding protein) is the most prominent with Dpo1 and also with Dpo4 as compared woth DNA polymerase Dpo2 and Dpo3
-
additional information
-
two factors are essential for efficient Pol V-mediated lesion bypass: 1. a DNA substrate onto which the beta-clamp is stably loaded and 2. an extended single-stranded RecA/ATP filament assembled downstream from the lesion site. For efficient bypass, Pol V needs to interact simultaneously with the beta-clamp and the 3' tip of the RecA filament
-
additional information
-
the DNA polymerase V is comprised by the UmuD'2C protein complex. Pol V activity depends on the beta-clamp and gamma-clamp loaders UmuC and UmuD'2, overview. Pol V shows robust activity on an SSB-coated circular DNA template in the presence of the beta/gamma-complex and a RecA nucleoprotein filament formed in trans
-
additional information
-
transcription from the promoter of the dinB gene is not significantly influenced by the DNA damage-inducing agent mitomycin C, thus mechanisms different from the classical RecA-dependent SOS response elevate Pol IV-dependent mutagenesis in starving Pseudomonas putida cells
-
additional information
-
the gap-filling activity of pol IV is not enhanced by a 5'-phosphate on the downstream primer but is stimulated by a 5'-terminal synthetic abasic site
-
additional information
-
no stimulation with poly(ethy1ene glycol)
-
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00012
2'-deoxyguanosine triphosphate
-
in 50 mM Tris-HCl (pH 7.6), 100 mM KCl, 5 mM MgCl2, 10% (v/v) glycerol, 1 mM dithiothreitol, at 30°C
0.0151
5-ethynyl-dCTP
-
pH and temperature not specified in the publication
0.0063
5-ethynyl-dUTP
-
pH and temperature not specified in the publication
0.006
5-phenyl-dCTP
-
pH and temperature not specified in the publication
0.0079
5-phenyl-dUTP
-
pH and temperature not specified in the publication
0.0141
5-vinyl-dCTP
-
pH and temperature not specified in the publication
0.0131
5-vinyl-dUTP
-
pH and temperature not specified in the publication
0.0003
5-[(1E)-3-[(4-[[(5-azido-2-nitrophenyl)carbonyl]amino]butanoyl)amino]prop-1-en-1-yl]uridine 5'-triphosphate
-
pH 9.0, 25°C
0.0055
5-[(1E)-3-{[(5-azido-2-nitrophenyl)carbonyl]amino}prop-1-en-1-yl]-2'-deoxyuridine 5'-triphosphate
-
pH 9.0, 25°C
0.04
5-[N-(2-nitro-5-azidobenzoyl)ami-nomethyl]-2'-deoxyuridine 5'-triphosphate
-
pH 9.0, 25°C
0.0125
7-deaza-dGTP
-
pH and temperature not specified in the publication
0.0073
7-ethynyl-7-deaza-dATP
-
pH and temperature not specified in the publication
0.0075
7-ethynyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
0.0061
7-methyl-7-deaza-dATP
-
pH and temperature not specified in the publication
0.0111
7-methyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
0.0056
7-phenyl-7-deaza-dATP
-
pH and temperature not specified in the publication
0.0041
7-phenyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
0.0109
7-vinyl-7-deaza-dATP
-
pH and temperature not specified in the publication
0.0095
7-vinyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
0.1056
dAMP:dA
-
37°C, pH 7.5, wild-type enzyme, substitution opposite the template A
-
0.551
dCMP:dA
-
37°C, pH 7.5, wild-type enzyme, substitution opposite the template A
-
2.091
dGMP:dA
-
37°C, pH 7.5, wild-type enzyme, substitution opposite the template A
-
0.16
dPTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
0.00003176
dTMP:dA
-
37°C, pH 7.5, wild-type enzyme, substitution opposite the template A
-
0.0032
TTP
-
pH and temperature not specified in the publication
0.006
2-aminopurine-2'-deoxy-D-ribose 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
0.0144
2-aminopurine-2'-deoxy-D-ribose 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
0.067
2-thio-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
0.98
2-thio-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with O6-methylguanine as template
0.013
5-Methyl-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
1.22
5-Methyl-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with O6-methylguanine as template
0.0011
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
0.0024
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of an nondamaged template
0.0028
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
0.297
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite an abasic site
0.344
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of a cis-syn thymine dimer of the template
1.153
dAMP:dG
-
37°C, pH 7.5, wild-type enzyme, substitution opposite the template G
-
1.42
dAMP:dG
-
37°C, pH 7.5, mutant enzyme D362A, substitution opposite the template G
-
0.0008
dATP
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
0.002
dATP
-
55°C, pH not specified in the publication, mutant enzyme L409M
0.0025
dATP
-
55°C, pH not specified in the publication, wild-type enzyme
0.0028
dATP
pH 7.5, 60°C, incorporation opposite the 3'-thymine of an nondamaged template
0.0032
dATP
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
0.007
dATP
pH 7.8, 37°C, dATP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.0087
dATP
-
pH and temperature not specified in the publication
0.0088
dATP
pH 7.8, 37°C, dATP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCGT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-TCAATCCTTACGAGCATCGCCCCC-3'
0.01
dATP
-
55°C, pH not specified in the publication, mutant enzyme A408S
0.012
dATP
-
55°C, pH not specified in the publication, mutant enzyme L409V
0.014
dATP
-
55°C, pH not specified in the publication, mutant enzyme L409I
0.02
dATP
pH 7.8, 37°C, incorporation of dATP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8ocoG)CACT-5'
0.022
dATP
pH 7.8, 37°C, dATP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.03
dATP
pH 7.8, 37°C, dATP insertion opposite an unmodified deoxyguanosine in 5'-TCGT-G-TCAATCCTTACGAGCATCGCCCCC-3'
0.046
dATP
-
55°C, pH not specified in the publication, mutant enzyme Y410V
0.069
dATP
-
55°C, pH not specified in the publication, mutant enzyme Y410L
0.13
dATP
-
55°C, pH not specified in the publication, mutant enzyme Y410I
0.18
dATP
pH 7.8, 37°C, incorporation of dATP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5'
0.205
dATP
pH 7.5, 60°C, incorporation opposite an abasic site
0.325
dATP
pH 7.5, 60°C, incorporation opposite the 3'-thymine of a cis-syn thymine dimer of the template
0.39
dATP
pH 7.5, 37°C, DNA polymerase Dpo3
0.43
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.59
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.69
dATP
pH 7.5, 37°C, DNA polymerase Dpo4
0.79
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.88
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
1.1
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
1.2
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
1.5
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
2.1
dATP
pH 7.5, 37°C, DNA polymerase Dpo1
2.2
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
2.3
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
2.5
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
2.8
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
3.2
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.00002772
dCMP:dG
-
37°C, pH 7.5, wild-type enzyme, substitution opposite the template G
-
0.00002847
dCMP:dG
-
37°C, pH 7.5, mutant enzyme D362A, substitution opposite the template G
-
0.000077
dCTP
pH 7.8, 37°C, dCTP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.000098
dCTP
pH 7.8, 37°C, dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.0002
dCTP
pH 7.8, 37°C, dCTP insertion opposite an unmodified deoxyguanosine in 5'-TCGT-G-TCAATCCTTACGAGCATCGCCCCC-3'
0.00044
dCTP
pH 7.8, 37°C, incorporation of dCTP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8ocoG)CACT-5'
0.00071
dCTP
pH 7.8, 37°C, dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCGT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-TCAATCCTTACGAGCATCGCCCCC-3'
0.00249
dCTP
-
mutant L606K, pH 7.5, 37°C, misincorporation of dTTP with G at first position
0.0041
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.00464
dCTP
-
wild-type enzyme, pH 7.5, 37°C, misincorporation of dTTP with G at first position
0.0062
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.0067
dCTP
-
pH and temperature not specified in the publication
0.0068
dCTP
-
template base: 2-fluoro-2'-deoxyinosine, pH 7.5, 37°C
0.0077
dCTP
pH 7.8, 37°C, incorporation of dCTP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5'
0.00792
dCTP
-
mutant L606G, pH 7.5, 37°C, misincorporation of dTTP with G at first position
0.0084
dCTP
pH 7.5, 37°C, DNA polymerase Dpo1
0.0098
dCTP
pH 7.5, 37°C, DNA polymerase Dpo2
0.01
dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
0.012
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.018
dCTP
pH 7.5, 37°C, dCTP insertion opposite the N6dA-butanetriol in 5'-TCTC-N6dA-butanetriol-GTTTATGGACCACC-3'
0.02
dCTP
pH 7.5, 37°C, dCTP insertion opposite the N6dA-(OH)2butyl-GSH in 5'-TCTC-N6dA-(OH)2butyl-GSH-GTTTATGGACCACC-3'
0.022
dCTP
pH 7.5, 37°C, dCTP insertion opposite an unmodified deoxyadenosine in 5'-TCTCAGTTTATGGACCACC-3'
0.026
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.027
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.039
dCTP
pH 7.5, 37°C, DNA polymerase Dpo4
0.045
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.052
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.075
dCTP
pH 7.5, 37°C, DNA polymerase Dpo3
0.13
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.773
dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with O6-methylguanine as template
0.83
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
1.2
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
1.3
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
2.4
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.00118
deoxynucleoside triphosphate
-
DNA polymerase lambda, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, and 0.1 mM EDTA, at 37°C
0.0014
deoxynucleoside triphosphate
wild type enzyme, in 50 mM Tris-HCl (pH 7.8), 1 mM dithiothreitol, at 25°C
0.0015
deoxynucleoside triphosphate
mutant enzyme R821A, in 50 mM Tris-HCl (pH 7.8), 1 mM dithiothreitol, at 25°C
0.002
deoxynucleoside triphosphate
mutant enzyme Y824A, in 50 mM Tris-HCl (pH 7.8), 1 mM dithiothreitol, at 25°C
0.0026
deoxynucleoside triphosphate
mutant enzyme R823A, in 50 mM Tris-HCl (pH 7.8), 1 mM dithiothreitol, at 25°C
0.003
deoxynucleoside triphosphate
pH 8.6, 75°C, mM of each nucleotide in an equimolar mixture of the four nucleotides, wild-type enzyme
0.003
deoxynucleoside triphosphate
pH 8.6, 75°C, mM of each nucleotide in an equimolar mixture of the four nucleotides, mutant enzyme H633R
0.00305
deoxynucleoside triphosphate
-
DNA polymerase beta, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, and 0.1 mM EDTA, at 37°C
0.0034
deoxynucleoside triphosphate
mutant enzyme R822A/Y824A in 50 mM Tris-HCl (pH 7.8), 1 mM dithiothreitol, at 25°C
0.0037
deoxynucleoside triphosphate
mutant enzyme R822A, in 50 mM Tris-HCl (pH 7.8), 1 mM dithiothreitol, at 25°C
0.17
deoxynucleoside triphosphate
-
pH 7.5, 75°C, KM-value of each nucleotide in an equimolar mixture of the four nucleotides, fusion protein of the Sso7d protein to the C-terminus of Tpa DNA polymerase
0.64
deoxynucleoside triphosphate
-
pH 7.5, 75°C, KM-value of each nucleotide in an equimolar mixture of the four nucleotides, unmodified Tpa DNA polymerase
0.263
dGMP:dG
-
37°C, pH 7.5, mutant enzyme D362A, substitution opposite the template G
-
0.3511
dGMP:dG
-
37°C, pH 7.5, wild-type enzyme, substitution opposite the template G
-
0.0053
dGTP
-
pH and temperature not specified in the publication
0.012
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.013
dGTP
pH 7.8, 37°C, dGTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.028
dGTP
pH 7.8, 37°C, incorporation of dGTP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8ocoG)CACT-5'
0.049
dGTP
pH 7.8, 37°C, dGCTP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.05
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.077
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.084
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.086
dGTP
pH 7.8, 37°C, incorporation of dGTP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5'
0.19
dGTP
pH 7.5, 37°C, DNA polymerase Dpo3
0.25
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.31
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.43
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.47
dGTP
pH 7.5, 37°C, DNA polymerase Dpo4
0.6
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
1.2
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
1.6
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
2.3
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
2.3
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
2.5
dGTP
pH 7.5, 37°C, DNA polymerase Dpo1
0.0000032
DNAn
-
pH 7.5, 75°C, template in the presence of an excess of annealed primer, fusion protein of the Sso7d protein to the C-terminus of Tpa DNA polymerase
0.0000057
DNAn
-
pH 7.5, 75°C, template in the presence of an excess of annealed primer, unmodified Tpa DNA polymerase
0.0000066
DNAn
pH 8.6, 75°C, mM of template, in the presence of an excess of annealed primer, mutant enzyme H633R
0.0000104
DNAn
pH 8.6, 75°C, mM of template, in the presence of an excess of annealed prime, wild-type enzyme
1.26
dTMP:dG
-
37°C, pH 7.5, wild-type enzyme, substitution opposite the template G
-
1.43
dTMP:dG
-
37°C, pH 7.5, mutant enzyme D362A, substitution opposite the template G
-
0.006
dTTP
pH 7.8, 37°C, dTTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.0093
dTTP
pH 7.5, 37°C, dTTP insertion opposite the N6dA-butanetriol in 5'-TCTC-N6dA-butanetriol-GTTTATGGACCACC-3'
0.0103
dTTP
pH 7.5, 37°C, dTTP insertion opposite an unmodified deoxyadenosine in 5'-TCTCAGTTTATGGACCACC-3'
0.013
dTTP
pH 7.5, 37°C, dTTP insertion opposite the N6dA-(OH)2butyl-GSH in 5'-TCTC-N6dA-(OH)2butyl-GSH-GTTTATGGACCACC-3'
0.029
dTTP
pH 7.8, 37°C, dTTP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.11
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.175
dTTP
-
wild-type enzyme, pH 7.5, 37°C, misincorporation of dTTP with G at first position
0.211
dTTP
-
mutant L606G, pH 7.5, 37°C, misincorporation of dTTP with G at first position
0.38
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.87
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.93
dTTP
pH 7.5, 37°C, DNA polymerase Dpo3
0.94
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.96
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
1.3
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
1.6
dTTP
pH 7.5, 37°C, DNA polymerase Dpo4
1.8
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
2.1
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
2.3
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
2.7
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
3.1
dTTP
pH 7.5, 37°C, DNA polymerase Dpo1
3.7
dTTP
pH 7.5, 37°C, DNA polymerase Dpo2
3.8
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
8.9
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.223
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite an abasic site
0.232
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
0.279
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of an nondamaged template
0.287
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of a cis-syn thymine dimer of the template
0.403
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
additional information
additional information
-
pre-steady state kinetics, and biphasic kinetics of nucleotide incorporation at 56°C
-
additional information
additional information
-
steady-state kinetics
-
additional information
additional information
-
biphasic kinetic analysis support a universal kinetic mechanism for the bypass of DNA double lesions, binding constants of the Dpo4-DNA binary complex, overview
-
additional information
additional information
steady-state kinetic parameters for single-base extension reactions by Dpo4 in the presence of either Ca2+ or Mg2+
-
additional information
additional information
-
steady-state kinetic parameters for single-base extension reactions by Dpo4 in the presence of either Ca2+ or Mg2+
-
additional information
additional information
steady-state kinetic parameters for one-base incorporation
-
additional information
additional information
-
steady-state kinetic parameters for one-base incorporation
-
additional information
additional information
steady-state kinetic parameters for one-base incorporation opposite G and N2-alkyl G adducts by Dpo4. Steady-state kinetic parameters for next base extension from G (or N2-alkyl G):C (or T) template primer termini by Dpo4
-
additional information
additional information
-
steady-state kinetic parameters for one-base incorporation opposite G and N2-alkyl G adducts by Dpo4. Steady-state kinetic parameters for next base extension from G (or N2-alkyl G):C (or T) template primer termini by Dpo4
-
additional information
additional information
-
kinetic parameters of several elementary steps for the forward polymerization reaction
-
additional information
additional information
-
steady-state kinetic parameters for next-base extension past 3-(2'-deoxy-beta-D-erythro-pentofuranosyl) pyrimido[1,2-alpha]purin-10(3H)-one
-
additional information
additional information
-
steady-state kinetic parameters for the single dNTP incorporation by Dpo4 T239W
-
additional information
additional information
-
steady-state kinetic parameters for dCTP incorporation by Dpo4 T239W
-
additional information
additional information
-
kinetic parameters for nucleotide incorporation by Sso pol B1 exo(-) at 55°C
-
additional information
additional information
-
pre-steady-state kinetic constants for dNTP and rNTP incorporation by wild-type and F12A mutant enzyme
-
additional information
additional information
pre-steady-state kinetic constants for dNTP and rNTP incorporation by wild-type and F12A mutant enzyme
-
additional information
additional information
-
transient state kinetic analyses of DNA polymerase beta, stopped flow absorbance assay development and kinetic modeling and simulations, overview. Pre-steady-state kinetic experiments measuring single nucleotide incorporation catalyzed by Pol beta are performed at 37°C, pH 7.1, over a range of both [Mg2+] and [Mg·dATP2?]. Rapid quench kinetics. Kinetics of nucleotide-induced subdomain closing
-
additional information
additional information
-
Michaelis-Menten kinetics and single nucleotide kinetics of wild-type and mutat enzymes, overview
-
additional information
additional information
-
kinetic constants for DNA-dependent and RNA-dependent DNA polymerization Michaelis-Menten mechanism and kinetic model of the mutant enzyme, overview
-
additional information
additional information
-
in pre-steady-state kinetic measurements, when temperature is raised from 22°C to 50°C, the rate (kpol) for cognate dTTP and non-cognate dATP nucleotide incorporations increases 6 and 4fold, respectively, whereas the Kd for both nucleotide incorporations changes only slightly. Single turnover kinetics
-
additional information
additional information
the reaction rate of M1pol exhibits a saturated profile of the Michaelis-Menten kinetics for dTTP concentrations but a substrate inhibition profile for poly(rA)-p(dT)45 concentrations
-
additional information
additional information
-
the reaction rate of K4polL329A exhibits a saturated profile of the Michaelis-Menten kinetics for dTTP concentrations but a substrate inhibition profile for poly(rA)-p(dT)45 concentrations
-
additional information
additional information
-
kinetics of nucleotide binding and incorporation, detailed overview. Weak binding is followed by a fast conformational change leading to much tighter binding, which is then followed by the chemical reaction, following the chemistry step, the enzyme shows fast release of diphosphate and then translocates to allow the binding of the next nucleotide, structure-function modeling. single turnover analysis shows that that the rate of the chemical reaction and the rate of diphosphate release are coincident
-
additional information
additional information
-
kinetics of nucleotide binding and incorporation, detailed overview. Weak binding is followed by a fast conformational change leading to much tighter binding, which is then followed by the chemical reaction, fast release of diphosphate, structure-function modeling
-
additional information
additional information
-
biphasic dissociation kinetics of the polymerase-DNA binary complex
-
additional information
additional information
-
pH 7.5, 50°C, Km is 0.71 mM for incorporation of dTTP in a 61mer template containing N6-furfuryl-deoxyadenosine
-
additional information
additional information
kinetic for nucleotide insertion opposite template cytosine
-
additional information
additional information
-
kinetic for nucleotide insertion opposite template cytosine
-
additional information
additional information
pH 7.5, 24°C, steady-state kinetic parameters for mispair extension by Dpo4
-
additional information
additional information
steady-state kinetic parameters for next base extension from G:C and AP site:A (or C) template:primer termini
-
additional information
additional information
-
steady-state kinetic parameters for next base extension from G:C and AP site:A (or C) template:primer termini
-
additional information
additional information
kinetic parameters for single dNTP incorporation opposite template 26-mer-N-(deoxyguanosin-8-yl)-1-aminopyrene
-
additional information
additional information
-
kinetic parameters for single dNTP incorporation opposite template 26-mer-N-(deoxyguanosin-8-yl)-1-aminopyrene
-
additional information
additional information
steady-state kinetic parameters for single-nucleotide incorporation opposite the C8- and N2-2-amino-3-methylimidazo[4,5-f]quinoline adducts of dGuo at the G3- and G1-positions of the NarI recognition sequence by Dpo4
-
additional information
additional information
-
steady-state parameters for the enzyme catalyzed insertion opposite and extension past O2-alkyl-dT
-
additional information
additional information
-
kinetic study of dNTP primer-extension opposite a benzo[a]pyrene-N2-dG-adduct with four DNA polymerases, including Sulfolobus solfataricus Dpo4 and Sulfolobus acidocaldarius Dbh. Vmax/Km is similar for correct dCTP insertion with Dpo4 and Dbh. Compared to Dpo4, Dbh misinsertion is slower for dATP (about 20fold), dGTP (about 110fold) and dTTP (about 6fold), due to decreases in Vmax. These findings provide support that Dbh is in the same Y-Family DNA polymerase class as eukaryotic DNA polymerase kappa and bacterial DNA polymerase IV, which accurately bypass N2-dG adducts
-
additional information
additional information
-
kinetic study of dNTP primer-extension opposite a benzo[a]pyrene-N2-dG-adduct with four DNA polymerases, including Sulfolobus solfataricus Dpo4 and Sulfolobus acidocaldarius Dbh. Vmax/Km is similar for correct dCTP insertion with Dpo4 and Dbh. Compared to Dpo4, Dbh misinsertion is slower for dATP (about 20fold), dGTP (about 110fold) and dTTP (about 6fold), due to decreases in Vmax. These findings provide support that Dbh is in the same Y-Family DNA polymerase class as eukaryotic DNA polymerase kappa and bacterial DNA polymerase IV, which accurately bypass N2-dG adducts
-
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
10.4
5-ethynyl-dCTP
-
pH and temperature not specified in the publication
4.6
5-ethynyl-dUTP
-
pH and temperature not specified in the publication
7.5
5-phenyl-dCTP
-
pH and temperature not specified in the publication
9.3
5-phenyl-dUTP
-
pH and temperature not specified in the publication
15.4
5-vinyl-dCTP
-
pH and temperature not specified in the publication
17.7
5-vinyl-dUTP
-
pH and temperature not specified in the publication
12.1
7-deaza-dGTP
-
pH and temperature not specified in the publication
6.3
7-ethynyl-7-deaza-dATP
-
pH and temperature not specified in the publication
17.5
7-ethynyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
5.5
7-methyl-7-deaza-dATP
-
pH and temperature not specified in the publication
12.7
7-methyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
13.5
7-phenyl-7-deaza-dATP
-
pH and temperature not specified in the publication
13.7
7-phenyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
7.1
7-vinyl-7-deaza-dATP
-
pH and temperature not specified in the publication
13.8
7-vinyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
0.05
dPTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
0.29
2-aminopurine-2'-deoxy-D-ribose 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
0.34
2-aminopurine-2'-deoxy-D-ribose 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
0.03
2-thio-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with O6-methylguanine as template
0.04
2-thio-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
0.02
5-Methyl-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with O6-methylguanine as template
0.33
5-Methyl-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
0.068
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of a cis-syn thymine dimer of the template
0.085
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite an abasic site
0.2
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
0.265
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
0.405
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of an nondamaged template
0.000016
dATP
pH 7.5, 37°C, DNA polymerase Dpo3
0.000083
dATP
pH 7.8, 37°C, incorporation of dATP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5'
0.0002
dATP
pH 7.8, 37°C, dATP insertion opposite N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.00024
dATP
pH 7.8, 37°C, dATP insertion opposite N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine in 5'-TCGT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-TCAATCCTTACGAGCATCGCCCCC-3'
0.00025
dATP
pH 7.8, 37°C, dATP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-G-GAATCCTTACGAGCATCGCCCCC-3'
0.00029
dATP
pH 7.8, 37°C, dATP insertion opposite an unmodified deoxyguanosine in 5'-TCGT-G-TCAATCCTTACGAGCATCGCCCCC-3'
0.0012
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0016
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.0017
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0018
dATP
pH 7.5, 37°C, DNA polymerase Dpo1
0.0025
dATP
pH 7.8, 37°C, incorporation of dATP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8oxoG)CACT-5'
0.0027
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.0028
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.0029
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.0036
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.0053
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.0068
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.0098
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.021
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.022
dATP
-
55°C, pH not specified in the publication, mutant enzyme L409I
0.028
dATP
-
55°C, pH not specified in the publication, mutant enzyme L409M
0.029
dATP
-
55°C, pH not specified in the publication, mutant enzyme Y410V
0.034
dATP
-
55°C, pH not specified in the publication, mutant enzyme L409V
0.037
dATP
-
55°C, pH not specified in the publication, mutant enzyme A408S
0.043
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.045
dATP
pH 7.5, 60°C, incorporation opposite the 3'-thymine of a cis-syn thymine dimer of the template
0.063
dATP
pH 7.5, 60°C, incorporation opposite an abasic site
0.073
dATP
pH 7.5, 37°C, DNA polymerase Dpo4
0.23
dATP
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
0.24
dATP
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
0.31
dATP
-
55°C, pH not specified in the publication, mutant enzyme Y410L
0.32
dATP
-
55°C, pH not specified in the publication, mutant enzyme Y410I
0.38
dATP
pH 7.5, 60°C, incorporation opposite the 3'-thymine of an nondamaged template
0.000053
dCTP
pH 7.5, 37°C, DNA polymerase Dpo2
0.0001
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.00024
dCTP
pH 7.8, 37°C, dCTP insertion opposite an unmodified deoxyguanosine in 5'-TCGT-G-TCAATCCTTACGAGCATCGCCCCC-3'
0.00027
dCTP
pH 7.8, 37°C, dCTP insertion opposite N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.0003
dCTP
pH 7.8, 37°C, dCTP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-G-GAATCCTTACGAGCATCGCCCCC-3'
0.00053
dCTP
pH 7.8, 37°C, dCTP insertion opposite N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine in 5'-TCGT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-TCAATCCTTACGAGCATCGCCCCC-3'
0.00053
dCTP
pH 7.5, 37°C, DNA polymerase Dpo3
0.0008
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0021
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.0022
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.005
dCTP
pH 7.8, 37°C, incorporation of dCTP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8oxoG)CACT-5'
0.0055
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.0057
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0062
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.013
dCTP
pH 7.8, 37°C, incorporation of dCTP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5'
0.02
dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with O6-methylguanine as template
0.022
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.027
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.038
dCTP
pH 7.5, 37°C, dCTP insertion opposite the N6dA-(OH)2butyl-GSH in 5'-TCTC-N6dA-(OH)2butyl-GSH-GTTTATGGACCACC-3'
0.042
dCTP
pH 7.5, 37°C, dCTP insertion opposite the N6dA-butanetriol in 5'-TCTC-N6dA-butanetriol-GTTTATGGACCACC-3'
0.044
dCTP
-
template base: 2-fluoro-2'-deoxyinosine, pH 7.5, 37°C
0.056
dCTP
pH 7.5, 37°C, dCTP insertion opposite an unmodified deoxyadenosine in 5'-TCTCAGTTTATGGACCACC-3'
0.065
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.092
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.23
dCTP
pH 7.5, 37°C, DNA polymerase Dpo1
0.28
dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
0.38
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
6.1
dCTP
-
pH and temperature not specified in the publication
12
dCTP
pH 7.5, 37°C, DNA polymerase Dpo4
1.05
deoxynucleoside triphosphate
-
equimolar mixture of all nucleotides, pH 7.5, 70°C
3.9
deoxynucleoside triphosphate
pH 8.6, 75°C, mM of each nucleotide in an equimolar mixture of the four nucleotides, wild-type enzyme
4.2
deoxynucleoside triphosphate
pH 8.6, 75°C, mM of each nucleotide in an equimolar mixture of the four nucleotides, mutant enzyme H633R
92
deoxynucleoside triphosphate
-
pH 7.5, 75°C, turnover number of each nucleotide in an equimolar mixture of the four nucleotides, unmodified Tpa DNA polymerase
116
deoxynucleoside triphosphate
-
pH 7.5, 75°C, turnover number of each nucleotide in an equimolar mixture of the four nucleotides, fusion protein of the Sso7d protein to the C-terminus of Tpa DNA polymerase
0.000013
dGTP
pH 7.5, 37°C, DNA polymerase Dpo3
0.0002
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.00032
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.00038
dGTP
pH 7.8, 37°C, incorporation of dGTP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8oxoG)CACT-5'
0.00043
dGTP
pH 7.8, 37°C, dGTP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-G-GAATCCTTACGAGCATCGCCCCC-3'
0.00055
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0006
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.0006
dGTP
pH 7.8, 37°C, dGTP insertion opposite N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.00068
dGTP
pH 7.8, 37°C, incorporation of dGTP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5'
0.0016
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.0033
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.0045
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.0049
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.0052
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.0067
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.0068
dGTP
pH 7.5, 37°C, DNA polymerase Dpo1
0.043
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.15
dGTP
pH 7.5, 37°C, DNA polymerase Dpo4
13.1
dGTP
-
pH and temperature not specified in the publication
2.4
DNAn
pH 8.6, 75°C, mM of template, in the presence of an excess of annealed primer, mutant enzyme H633R
2.6
DNAn
pH 8.6, 75°C, mM of template, in the presence of an excess of annealed primer, wild-type enzyme
12.9
DNAn
-
pH 7.5, 75°C, mol of template, in the presence of an excess of annealed primer, fusion protein of the Sso7d protein to the C-terminus of Tpa DNA polymerase
13.6
DNAn
-
pH 7.5, 75°C, mol of template, in the presence of an excess of annealed primer, unmodified Tpa DNA polymerase
0.0000072
dTTP
pH 7.5, 37°C, DNA polymerase Dpo2
0.00011
dTTP
pH 7.5, 37°C, DNA polymerase Dpo3
0.00013
dTTP
pH 7.8, 37°C, dTTP insertion opposite N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.00019
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.00029
dTTP
pH 7.8, 37°C, dTTP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-G-GAATCCTTACGAGCATCGCCCCC-3'
0.0004
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.0021
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.0023
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.003
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0046
dTTP
-
template base: 2-bromo-2'-deoxyinosine, pH 7.5, 37°C
0.0047
dTTP
-
template base: 2-fluoro-2'-deoxyinosine, pH 7.5, 37°C
0.012
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.014
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.017
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.021
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.025
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.025
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.043
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.063
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.096
dTTP
pH 7.5, 37°C, DNA polymerase Dpo1
0.28
dTTP
pH 7.5, 37°C, dTTP insertion opposite the N6dA-butanetriol in 5'-TCTC-N6dA-butanetriol-GTTTATGGACCACC-3'
0.35
dTTP
pH 7.5, 37°C, dTTP insertion opposite the N6dA-(OH)2butyl-GSH in 5'-TCTC-N6dA-(OH)2butyl-GSH-GTTTATGGACCACC-3'
0.36
dTTP
pH 7.5, 37°C, dTTP insertion opposite an unmodified deoxyadenosine in 5'-TCTCAGTTTATGGACCACC-3'
0.48
dTTP
pH 7.5, 37°C, DNA polymerase Dpo4
0.012
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of a cis-syn thymine dimer of the template
0.028
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite an abasic site
0.063
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
0.145
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
0.15
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of an nondamaged template
0.000042
primed M13
-
exonuclease activity, D190A mutant, pH 7.6, 37°C
-
additional information
additional information
DNA polymerase IV (Dpo4) shows 90-fold higher incorporation efficiency of dCTP > dATP opposite 8-oxoG and 4-fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. Extension beyond an 8-oxoG:C pair is similar to G:C and faster than for an 8-oxoG:A pair, in contrast to other polymerases. dCTP insertion opposite 8-oxoG was lower than for opposite guanine
-
additional information
additional information
-
DNA polymerase IV (Dpo4) shows 90-fold higher incorporation efficiency of dCTP > dATP opposite 8-oxoG and 4-fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. Extension beyond an 8-oxoG:C pair is similar to G:C and faster than for an 8-oxoG:A pair, in contrast to other polymerases. dCTP insertion opposite 8-oxoG was lower than for opposite guanine
-
additional information
additional information
steady-state kinetic parameters for single-base extension reactions by Dpo4 in the presence of either Ca2+ or Mg2+
-
additional information
additional information
-
steady-state kinetic parameters for single-base extension reactions by Dpo4 in the presence of either Ca2+ or Mg2+
-
additional information
additional information
steady-state kinetic parameters for one-base incorporation
-
additional information
additional information
-
steady-state kinetic parameters for one-base incorporation
-
additional information
additional information
steady-state kinetic parameters for one-base incorporation opposite G and N2-alkyl G adducts by Dpo4. Steady-state kinetic parameters for next base extension from G (or N2-alkyl G):C (or T) template primer termini by Dpo4
-
additional information
additional information
-
steady-state kinetic parameters for one-base incorporation opposite G and N2-alkyl G adducts by Dpo4. Steady-state kinetic parameters for next base extension from G (or N2-alkyl G):C (or T) template primer termini by Dpo4
-
additional information
additional information
-
steady-state kinetic parameters for the single dNTP incorporation by Dpo4 T239W
-
additional information
additional information
-
steady-state kinetic parameters for dCTP incorporation by Dpo4 T239W
-
additional information
additional information
the fidelity of nucleotide incorporation by Dpo3 from the polymerase active site alone is 1000-10000 at 37°C. The functional exonuclease proofreading active site will increase fidelity by at least 100
-
additional information
additional information
-
the fidelity of nucleotide incorporation by Dpo3 from the polymerase active site alone is 1000-10000 at 37°C. The functional exonuclease proofreading active site will increase fidelity by at least 100
-
additional information
additional information
-
pre-steady-state kinetic constants for dNTP and rNTP incorporation by wild-type and F12A mutant enzyme
-
additional information
additional information
pre-steady-state kinetic constants for dNTP and rNTP incorporation by wild-type and F12A mutant enzyme
-
additional information
additional information
-
Tpa-S DNA polymerase (the fusion of the Sso7d protein to the C-terminus of Tpa DNA polymerase) has nearly an identical turnover rate for DNA with the unmodified Tpa DNA polymerase. However, Tpa-S DNA polymerase has a somewhat higher (about 1.26fold) turnover rate in nucleotide incorporation than Tpa DNA polymerase
-
additional information
additional information
-
pH 7.5, 50°C, kcat is 0.16/s for incorporation of dTTP in a 61mer template containing N6-furfuryl-deoxyadenosine
-
additional information
additional information
kinetic for nucleotide insertion opposite template cytosine
-
additional information
additional information
-
kinetic for nucleotide insertion opposite template cytosine
-
additional information
additional information
pH 7.5, 24°C, steady-state kinetic parameters for mispair extension by Dpo4
-
additional information
additional information
steady-state kinetic parameters for next base extension from G:C and AP site:A (or C) template:primer termini
-
additional information
additional information
-
steady-state kinetic parameters for next base extension from G:C and AP site:A (or C) template:primer termini
-
additional information
additional information
kinetic parameters for single dNTP incorporation opposite template 26-mer-N-(deoxyguanosin-8-yl)-1-aminopyrene
-
additional information
additional information
-
kinetic parameters for single dNTP incorporation opposite template 26-mer-N-(deoxyguanosin-8-yl)-1-aminopyrene
-
additional information
additional information
steady-state kinetic parameters for single-nucleotide incorporation opposite the C8- and N2-2-amino-3-methylimidazo[4,5-f]quinoline adducts of dGuo at the G3- and G1-positions of the NarI recognition sequence by Dpo4
-
additional information
additional information
-
steady-state parameters for the enzyme catalyzed insertion opposite and extension past O2-alkyl-dT
-
additional information
additional information
the average speed of utilization of dNTPs by the Taq polymerase is kcat: 47/s
-
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
690
5-ethynyl-dCTP
-
pH and temperature not specified in the publication
730
5-ethynyl-dUTP
-
pH and temperature not specified in the publication
1250
5-phenyl-dCTP
-
pH and temperature not specified in the publication
1180
5-phenyl-dUTP
-
pH and temperature not specified in the publication
1100
5-vinyl-dCTP
-
pH and temperature not specified in the publication
1350
5-vinyl-dUTP
-
pH and temperature not specified in the publication
970
7-deaza-dGTP
-
pH and temperature not specified in the publication
880
7-ethynyl-7-deaza-dATP
-
pH and temperature not specified in the publication
2330
7-ethynyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
900
7-methyl-7-deaza-dATP
-
pH and temperature not specified in the publication
1140
7-methyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
2410
7-phenyl-7-deaza-dATP
-
pH and temperature not specified in the publication
3340
7-phenyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
650
7-vinyl-7-deaza-dATP
-
pH and temperature not specified in the publication
1450
7-vinyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
0.31
dPTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
2060
TTP
-
pH and temperature not specified in the publication
20.14
2-aminopurine-2'-deoxy-D-ribose 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
56.7
2-aminopurine-2'-deoxy-D-ribose 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
0.03
2-thio-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with O6-methylguanine as template
0.6
2-thio-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
0.016
5-Methyl-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with O6-methylguanine as template
25.38
5-Methyl-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
0.2
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of a cis-syn thymine dimer of the template
0.29
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite an abasic site
71.4
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
168.7
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of an nondamaged template
240.9
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
0.000000041
dATP
pH 7.5, 37°C, DNA polymerase Dpo3
0.00000086
dATP
pH 7.5, 37°C, DNA polymerase Dpo1
0.00011
dATP
pH 7.5, 37°C, DNA polymerase Dpo4
0.00046
dATP
pH 7.8, 37°C, incorporation of dATP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5'
0.001
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0011
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.0011
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0016
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.0021
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.0022
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.0026
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.0032
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.0034
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.0043
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.01
dATP
pH 7.8, 37°C, dATP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.01
dATP
pH 7.8, 37°C, dATP insertion opposite an unmodified deoxyguanosine in 5'-TCGT-G-TCAATCCTTACGAGCATCGCCCCC-3'
0.02
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.03
dATP
pH 7.8, 37°C, dATP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.03
dATP
pH 7.8, 37°C, dATP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCGT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-TCAATCCTTACGAGCATCGCCCCC-3'
0.099
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.125
dATP
pH 7.8, 37°C, incorporation of dATP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8ocoG)CACT-5'
0.138
dATP
pH 7.5, 60°C, incorporation opposite the 3'-thymine of a cis-syn thymine dimer of the template
0.31
dATP
pH 7.5, 60°C, incorporation opposite an abasic site
75
dATP
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
235.7
dATP
pH 7.5, 60°C, incorporation opposite the 3'-thymine of an nondamaged template
287.5
dATP
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
990
dATP
-
pH and temperature not specified in the publication
0.0000054
dCTP
pH 7.5, 37°C, DNA polymerase Dpo2
0.0000071
dCTP
pH 7.5, 37°C, DNA polymerase Dpo3
0.000042
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.0025
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.0061
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0095
dCTP
-
template base: 2-bromo-2'-deoxyinosine, pH 7.5, 37°C
0.019
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.021
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.026
dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with O6-methylguanine as template
0.027
dCTP
pH 7.5, 37°C, DNA polymerase Dpo1
0.083
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.11
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.12
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.31
dCTP
pH 7.5, 37°C, DNA polymerase Dpo4
0.7
dCTP
pH 7.8, 37°C, dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCGT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-TCAATCCTTACGAGCATCGCCCCC-3'
1.2
dCTP
pH 7.8, 37°C, dCTP insertion opposite an unmodified deoxyguanosine in 5'-TCGT-G-TCAATCCTTACGAGCATCGCCCCC-3'
1.7
dCTP
pH 7.8, 37°C, incorporation of dCTP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5'
1.9
dCTP
pH 7.5, 37°C, dCTP insertion opposite the N6dA-(OH)2butyl-GSH in 5'-TCTC-N6dA-(OH)2butyl-GSH-GTTTATGGACCACC-3'
2.3
dCTP
pH 7.5, 37°C, dCTP insertion opposite the N6dA-butanetriol in 5'-TCTC-N6dA-butanetriol-GTTTATGGACCACC-3'
2.4
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
2.5
dCTP
pH 7.5, 37°C, dCTP insertion opposite an unmodified deoxyadenosine in 5'-TCTCAGTTTATGGACCACC-3'
2.8
dCTP
pH 7.8, 37°C, dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
3.9
dCTP
pH 7.8, 37°C, dCTP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
11
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
11.36
dCTP
pH 7.8, 37°C, incorporation of dCTP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8ocoG)CACT-5'
23
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
28
dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
31
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
910
dCTP
-
pH and temperature not specified in the publication
0.000000068
dGTP
pH 7.5, 37°C, DNA polymerase Dpo3
0.0000027
dGTP
pH 7.5, 37°C, DNA polymerase Dpo1
0.00032
dGTP
pH 7.5, 37°C, DNA polymerase Dpo4
0.0004
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.00064
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0029
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.0055
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.0065
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.008
dGTP
pH 7.8, 37°C, incorporation of dGTP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5'
0.01
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.01
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.01
dGTP
pH 7.8, 37°C, dGTP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.014
dGTP
pH 7.8, 37°C, incorporation of dGTP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8ocoG)CACT-5'
0.019
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.019
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.027
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.03
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.05
dGTP
pH 7.8, 37°C, dGTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.062
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
2470
dGTP
-
pH and temperature not specified in the publication
0.0000000019
dTTP
pH 7.5, 37°C, DNA polymerase Dpo2
0.00000012
dTTP
pH 7.5, 37°C, DNA polymerase Dpo3
0.000031
dTTP
pH 7.5, 37°C, DNA polymerase Dpo1
0.00017
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.0003
dTTP
pH 7.5, 37°C, DNA polymerase Dpo4
0.0012
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.0016
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.0026
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0028
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.0031
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0046
dTTP
-
template base: 2-bromo-2'-deoxyinosine, pH 7.5, 37°C
0.0081
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.01
dTTP
pH 7.8, 37°C, dTTP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.016
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.017
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.019
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.02
dTTP
pH 7.8, 37°C, dTTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.022
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.024
dTTP
-
template base: 2-fluoro-2'-deoxyinosine, pH 7.5, 37°C
0.037
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
26.9
dTTP
pH 7.5, 37°C, dTTP insertion opposite the N6dA-(OH)2butyl-GSH in 5'-TCTC-N6dA-(OH)2butyl-GSH-GTTTATGGACCACC-3'
30
dTTP
pH 7.5, 37°C, dTTP insertion opposite the N6dA-butanetriol in 5'-TCTC-N6dA-butanetriol-GTTTATGGACCACC-3'
35
dTTP
pH 7.5, 37°C, dTTP insertion opposite an unmodified deoxyadenosine in 5'-TCTCAGTTTATGGACCACC-3'
0.04
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of a cis-syn thymine dimer of the template
0.13
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite an abasic site
0.156
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
0.54
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of an nondamaged template
0.625
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
additional information
additional information
DNA polymerase IV (Dpo4) shows 90-fold higher incorporation efficiency of dCTP > dATP opposite 8-oxoG and 4-fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. Extension beyond an 8-oxoG:C pair is similar to G:C and faster than for an 8-oxoG:A pair, in contrast to other polymerases. dCTP insertion opposite 8-oxoG was lower than for opposite guanine
-
additional information
additional information
-
DNA polymerase IV (Dpo4) shows 90-fold higher incorporation efficiency of dCTP > dATP opposite 8-oxoG and 4-fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. Extension beyond an 8-oxoG:C pair is similar to G:C and faster than for an 8-oxoG:A pair, in contrast to other polymerases. dCTP insertion opposite 8-oxoG was lower than for opposite guanine
-
additional information
additional information
steady-state kinetic parameters for single-base extension reactions by Dpo4 in the presence of either Ca2+ or Mg2+
-
additional information
additional information
-
steady-state kinetic parameters for single-base extension reactions by Dpo4 in the presence of either Ca2+ or Mg2+
-
additional information
additional information
steady-state kinetic parameters for one-base incorporation
-
additional information
additional information
-
steady-state kinetic parameters for one-base incorporation
-
additional information
additional information
transient-state kinetic analysis of Dpo4 mutants and dATP Incorporation opposite 8-oxoG.Transient-state kinetic analysis of Dpo4 mutants and dCTP incorporation opposite 8-oxoG
-
additional information
additional information
-
transient-state kinetic analysis of Dpo4 mutants and dATP Incorporation opposite 8-oxoG.Transient-state kinetic analysis of Dpo4 mutants and dCTP incorporation opposite 8-oxoG
-
additional information
additional information
steady-state kinetic parameters for one-base incorporation opposite G and N2-alkyl G adducts by Dpo4. Steady-state kinetic parameters for next base extension from G (or N2-alkyl G):C (or T) template primer termini by Dpo4
-
additional information
additional information
-
steady-state kinetic parameters for one-base incorporation opposite G and N2-alkyl G adducts by Dpo4. Steady-state kinetic parameters for next base extension from G (or N2-alkyl G):C (or T) template primer termini by Dpo4
-
additional information
additional information
-
steady-state kinetic parameters for the single dNTP incorporation by Dpo4 T239W
-
additional information
additional information
-
steady-state kinetic parameters for dCTP incorporation by Dpo4 T239W
-
additional information
additional information
-
pre-steady-state kinetic constants for dNTP and rNTP incorporation by wild-type and F12A mutant enzyme
-
additional information
additional information
pre-steady-state kinetic constants for dNTP and rNTP incorporation by wild-type and F12A mutant enzyme
-
additional information
additional information
-
pH 7.5, 50°C, kcat/Km is 0.0225/s * mM for incorporation of dTTP in a 61mer template containing N6-furfuryl-deoxyadenosine
-
additional information
additional information
kinetic for nucleotide insertion opposite template cytosine
-
additional information
additional information
-
kinetic for nucleotide insertion opposite template cytosine
-
additional information
additional information
pH 7.5, 24°C, steady-state kinetic parameters for mispair extension by Dpo4
-
additional information
additional information
steady-state kinetic parameters for next base extension from G:C and AP site:A (or C) template:primer termini
-
additional information
additional information
-
steady-state kinetic parameters for next base extension from G:C and AP site:A (or C) template:primer termini
-
additional information
additional information
kinetic parameters for single dNTP incorporation opposite template 26-mer-N-(deoxyguanosin-8-yl)-1-aminopyrene
-
additional information
additional information
-
kinetic parameters for single dNTP incorporation opposite template 26-mer-N-(deoxyguanosin-8-yl)-1-aminopyrene
-
additional information
additional information
steady-state kinetic parameters for single-nucleotide incorporation opposite the C8- and N2-2-amino-3-methylimidazo[4,5-f]quinoline adducts of dGuo at the G3- and G1-positions of the NarI recognition sequence by Dpo4
-
additional information
additional information
-
steady-state parameters for the enzyme catalyzed insertion opposite and extension past O2-alkyl-dT
-
additional information
additional information
DNA synthesis from dNDPs is a little over an order of magnitude lower than from dNTPs and that Vmax/KM is about 400 times lower for dNDPs than for dNTPs
-
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00054
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
pH 7.5, 30°C
0.0018 - 0.068
2-thiomethyl-6-phenyl-4-(4'-hydroxybutyl)-1,2,4,-triazole (5,1-C)(1,2,4)triazine-7-one triphosphate
0.0001
6-chloro-1,4-dihydro-4-oxo-1-(beta-D-ribofuranosyl) quinoline-3-carboxylic acid
-
in 50 mM Tris-HCl (pH 8.0), 8 mM MgCl2, and 0.5 mM dithiohtreitol, at 37°C
0.0002
6-chloro-1,4-dihydro-4-oxo-1H-quinoline-3-carboxylic acid
-
in 50 mM Tris-HCl (pH 8.0), 8 mM MgCl2, and 0.5 mM dithiohtreitol, at 37°C
0.0004
acyclovir triphosphate
-
in 50 mM Tris-HCl (pH 8.0), 8 mM MgCl2, and 0.5 mM dithiohtreitol, at 37°C
0.0144
N-(2,4-dinitro-5-fluorophenyl)-2-aminoethyl triphosphate
-
mutant enzyme Y505A
0.0005
N-(2,4-dinitro-5-imidazolylphenyl)-2-aminoethyl triphosphate
-
mutant enzyme Y505A
0.0154
N-(2,4-dinitro-5-imidazolylphenyl)-4-aminobutyl triphosphate
-
mutant enzyme Y505A
0.0091
N-[6-N-(2,4-dinitrophenyl)aminohexanoyl]-2-aminoethyl triphosphate
-
mutant enzyme Y505A
0.00082
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
pH 7.5, 30°C
0.0028
(9-adenylmethylcarbonyl)-4-aminobutyl triphosphate
-
37°C, pH 7.0, wild-type enzyme
0.0038
(9-adenylmethylcarbonyl)-4-aminobutyl triphosphate
-
37°C, pH 7.0, mutant enzyme Y505A
0.0004
(biphenylcarbonyl)-4-oxobutyl triphosphate
-
37°C, pH 7.0, mutant enzyme Y505A
0.0011
(biphenylcarbonyl)-4-oxobutyl triphosphate
-
37°C, pH 7.0, wild-type enzyme
0.0048
(biphenylcarbonyl)-4-oxobutyl triphosphate
-
37°C, pH 7.0, wild-type enzyme
0.0018
2-thiomethyl-6-phenyl-4-(4'-hydroxybutyl)-1,2,4,-triazole (5,1-C)(1,2,4)triazine-7-one triphosphate
-
37°C, pH 7.0, mutant enzyme Y505A
0.0027
2-thiomethyl-6-phenyl-4-(4'-hydroxybutyl)-1,2,4,-triazole (5,1-C)(1,2,4)triazine-7-one triphosphate
-
37°C, pH 7.0, wid-type enzyme
0.068
2-thiomethyl-6-phenyl-4-(4'-hydroxybutyl)-1,2,4,-triazole (5,1-C)(1,2,4)triazine-7-one triphosphate
-
37°C, pH 7.0, wid-type enzyme
0.0003
aphidicolin
-
in 50 mM Tris-HCl (pH 8.0), 8 mM MgCl2, and 0.5 mM dithiohtreitol, at 37°C
0.0031
N-(2,4-dinitro-5-fluorophenyl)-4-aminobutyl triphosphate
-
37°C, pH 7.0, wild-type enzyme
0.0065
N-(2,4-dinitro-5-fluorophenyl)-4-aminobutyl triphosphate
-
37°C, pH 7.0, mutant enzyme Y505A
0.0012
N-(2,4-dinitrophenyl)-4-aminobutyl triphosphate
-
37°C, pH 7.0, wild-type enzyme
0.0035
N-(2,4-dinitrophenyl)-4-aminobutyl triphosphate
-
37°C, pH 7.0, mutant enzyme Y505A
0.0016
N-(benzyloxycarbonyl)-4-aminobutyl triphosphate
-
37°C, pH 7.0, mutant enzyme Y505A
0.0017
N-(benzyloxycarbonyl)-4-aminobutyl triphosphate
-
37°C, pH 7.0, wild-type enzyme
0.07
N-(benzyloxycarbonyl)-4-aminobutyl triphosphate
-
37°C, pH 7.0, wild-type enzyme
additional information
additional information
-
Allium sativum extract has an KI value of 0.0112 mM using DNA polymerase lambda, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, and 0.1 mM EDTA, at 37°C
-
additional information
additional information
-
Allium sativum extract has a KI value of 0.00368 mM using DNA polymerase beta, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, and 0.1 mM EDTA, at 37°C
-
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.011 - 0.1
(2E)-2-(3-nitro-4-[[6-(trifluoromethyl)pyridin-3-yl]sulfanyl]benzylidene)-5-thioxo-1,3-thiazolidin-4-one
0.0083 - 0.08
(5Z)-5-[3-bromo-4-[(4-fluorophenyl)sulfanyl]benzylidene]-2-thioxo-1,3-thiazolidin-4-one
0.0093 - 0.1
(5Z)-5-[4-(4-methylphenoxy)-3-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
0.0059 - 0.0644
(5Z)-5-[4-[(4-fluorobenzyl)oxy]benzylidene]-2-thioxo-1,3-thiazolidin-4-one
0.0598
1-deoxyrubralactone
Homo sapiens
-
in 50 mM Tris-HCl (pH 7.5) containing 1 mM dithiothreitol, 50% (v/v) glycerol, and 0.1 mM EDTA, at 37°C
0.0124 - 0.0888
4-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl 2-chlorobenzoate
0.0081 - 0.0429
5-[2-[(4-chlorophenyl)sulfanyl]-5-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
0.01 - 0.0455
5-[2-[(4-methylphenyl)sulfanyl]-5-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
0.0038
epigallocatechin gallate
Homo sapiens
-
pH and temperature not specified in the publication
0.006
vitamin K3
Homo sapiens
-
isozyme pol gamma, in 50 mM Tris-HCl (pH 7.5) containing 1 mM dithiothreitol, 50% (v/v) glycerol, and 0.1 mM EDTA, at 37°C
0.011
(2E)-2-(3-nitro-4-[[6-(trifluoromethyl)pyridin-3-yl]sulfanyl]benzylidene)-5-thioxo-1,3-thiazolidin-4-one
Homo sapiens
-
pH and temperature not specified in the publication, inhibition of DNA Pol lambda
0.1
(2E)-2-(3-nitro-4-[[6-(trifluoromethyl)pyridin-3-yl]sulfanyl]benzylidene)-5-thioxo-1,3-thiazolidin-4-one
Homo sapiens
-
above, pH and temperature not specified in the publication, inhibition of DNA Pol beta
0.0083
(5Z)-5-[3-bromo-4-[(4-fluorophenyl)sulfanyl]benzylidene]-2-thioxo-1,3-thiazolidin-4-one
Homo sapiens
-
pH and temperature not specified in the publication, inhibition of DNA Pol lambda
0.08
(5Z)-5-[3-bromo-4-[(4-fluorophenyl)sulfanyl]benzylidene]-2-thioxo-1,3-thiazolidin-4-one
Homo sapiens
-
pH and temperature not specified in the publication, inhibition of DNA Pol beta
0.0093
(5Z)-5-[4-(4-methylphenoxy)-3-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
Homo sapiens
-
pH and temperature not specified in the publication, inhibition of DNA Pol lambda
0.1
(5Z)-5-[4-(4-methylphenoxy)-3-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
Homo sapiens
-
above, pH and temperature not specified in the publication, inhibition of DNA Pol beta
0.0059
(5Z)-5-[4-[(4-fluorobenzyl)oxy]benzylidene]-2-thioxo-1,3-thiazolidin-4-one
Homo sapiens
-
pH and temperature not specified in the publication, inhibition of DNA Pol lambda
0.0644
(5Z)-5-[4-[(4-fluorobenzyl)oxy]benzylidene]-2-thioxo-1,3-thiazolidin-4-one
Homo sapiens
-
pH and temperature not specified in the publication, inhibition of DNA Pol beta
0.092
1,2-bis[methylsulfonyl]-1-[(methylamino)carbonyl]hydrazine
Homo sapiens
-
Pol beta, at 25°C, pH 8.0
0.307
1,2-bis[methylsulfonyl]-1-[(methylamino)carbonyl]hydrazine
Homo sapiens
-
Klenow fragment, at 25°C, pH 8.0
0.0124
4-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl 2-chlorobenzoate
Homo sapiens
-
pH and temperature not specified in the publication, inhibition of DNA Pol lambda
0.0888
4-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl 2-chlorobenzoate
Homo sapiens
-
pH and temperature not specified in the publication, inhibition of DNA Pol beta
0.0081
5-[2-[(4-chlorophenyl)sulfanyl]-5-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
Homo sapiens
-
pH and temperature not specified in the publication, inhibition of DNA Pol lambda
0.0429
5-[2-[(4-chlorophenyl)sulfanyl]-5-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
Homo sapiens
-
pH and temperature not specified in the publication, inhibition of DNA Pol beta
0.01
5-[2-[(4-methylphenyl)sulfanyl]-5-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
Homo sapiens
-
pH and temperature not specified in the publication, inhibition of DNA Pol lambda
0.0455
5-[2-[(4-methylphenyl)sulfanyl]-5-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
Homo sapiens
-
pH and temperature not specified in the publication, inhibition of DNA Pol beta
0.115
diallyl trisulfide
Rattus norvegicus
-
DNA polymerase beta, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, and 0.1 mM EDTA, at 37°C
0.146
diallyl trisulfide
Homo sapiens
-
DNA polymerase lambda, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, and 0.1 mM EDTA, at 37°C
0.0023
pyranicin
Homo sapiens
-
DNA polymerase lambda, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, 0.1 mM EDTA, at 37°C
0.0053
pyranicin
Bos taurus
-
in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, 0.1 mM EDTA, at 37°C
0.0059
pyranicin
Homo sapiens
-
DNA polymerase gamma, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, 0.1 mM EDTA, at 37°C
0.0065
pyranicin
Drosophila melanogaster
-
DNA polymerase alpha, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, 0.1 mM EDTA, at 37°C
0.0084
pyranicin
Homo sapiens
-
DNA polymerase delta, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, 0.1 mM EDTA, at 37°C
0.0088
pyranicin
Oncorhynchus masou
-
in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, 0.1 mM EDTA, at 37°C
0.0089
pyranicin
Drosophila melanogaster
-
DNA polymerase delta, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, 0.1 mM EDTA, at 37°C
0.0096
pyranicin
Rattus norvegicus
-
in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, 0.1 mM EDTA, at 37°C
0.0102
pyranicin
Homo sapiens
-
DNA polymerase eta, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, 0.1 mM EDTA, at 37°C
0.0111
pyranicin
Homo sapiens
-
DNA polymerase kappa, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, 0.1 mM EDTA, at 37°C
0.013
pyranicin
Homo sapiens
-
DNA polymerase iota, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, 0.1 mM EDTA, at 37°C
0.014
pyranicin
Drosophila melanogaster
-
DNA polymerase epsilon, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, 0.1 mM EDTA, at 37°C
0.0158
pyranicin
Homo sapiens
-
DNA polymerase epsilon, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, 0.1 mM EDTA, at 37°C
0.2
pyranicin
Brassica oleracea
-
IC50 above 0.2 mM, DNA polymerase I, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, 0.1 mM EDTA, at 37°C
0.2
pyranicin
Brassica oleracea
-
IC50 above 0.2 mM, DNA polymerase II, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, 0.1 mM EDTA, at 37°C
0.2
pyranicin
Escherichia coli
-
IC50 above 0.2 mM, DNA polymerase I, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, 0.1 mM EDTA, at 37°C
0.2
pyranicin
Thermus aquaticus
-
IC50 above 0.2 mM, DNA polymerase I, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, 0.1 mM EDTA, at 74°C
0.2
pyranicin
Tequatrovirus T4
-
IC50 above 0.2 mM, DNA polymerase I, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, 0.1 mM EDTA, at 37°C
additional information
additional information
Homo sapiens
-
Allium sativum extract has an IC50 of 0.0345 mM, using DNA polymerase lambda in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, and 0.1 mM EDTA, at 37°C
-
additional information
additional information
Rattus norvegicus
-
Allium sativum extract has an IC50 value of 0.0097 mM using DNA polymerase beta, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, and 0.1 mM EDTA, at 37°C
-
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.027
20
9.84
additional information
additional information
quantitative analysis of DNA- and RNA-dependent DNA polymerase activity of enzyme mutants, overview
additional information
the purified recombinant Taq DNA polymerase shows better performance in comparison to commercially available polymerases
additional information
-
the purified recombinant Taq DNA polymerase shows better performance in comparison to commercially available polymerases
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6.5
7 - 8.5
maximal activity is observed with 20 mM Tris between pH 7 and 8.5
7.2
7.5
7.5 - 8.5
7.8
7.8 - 8.2
8 - 8.5
8 - 9
8.2
8.5
8.5 - 9
8.8
8.5
recombinant enzyme with the nonspecific DNA-binding protein Sso7d from Sulfolobus solfataricus fused to the C-terminus
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5.5 - 6.5
pH 5.5: about 50% of maximal activity, pH 6.5: about 50% of maximal activity
5.5 - 8
pH 5.5: about 70% of maximal activity, pH 8.0: about 20% of maximal activity, maximal activity in 50 mM potassium phosphate buffer
6 - 7.5
pH 6.5: about 65% of maximal activity, pH 9.2: about 20% of maximal activity, potassium phosphate buffer
6 - 9
pH 6.0: about 30% of maximal activity, pH 9.0: about 75% of maximal activity
6.5 - 7.5
-
pH 6.5: about 60% of maximal activity, pH 7.5: about 89% of maximal activity
6.5 - 8.5
6.5 - 8.8
pH 6.5: about 65% of maximal activity, pH 8.8: about 50% of maximal activity
6.5 - 9
7 - 8.8
pH 7.0: about 75% of maximal activity, pH 8.8: about 75% of maximal activity
7 - 9
pH 7.0: about 50% of maximal activity, pH 9.0: about 60% of maximal activity
7 - 9.5
pH 7.0: about 70% of maximal activity, pH 9.5: about 70% of maximal activity, in 50 mM Tris-HCl buffer
7.2 - 9
-
pH 7.2: about 65% of maximal activity, pH 9.0: about 40% of maximal activity
6.5 - 8.5
-
pH 6.5: about 50% of maximal activity, pH 8.5: about 40% of maximal activity
6.5 - 9
-
pH 6.5: about 70% of maximal activity, pH 9.0: about 70% of maximal activity
6.5 - 9
pH 6.5: about 55% of maximal activity, pH 9.0: about 90% of maximal activity, recombinant enzyme with the nonspecific DNA-binding protein Sso7d from Sulfolobus solfataricus fused to the C-terminus
6.5 - 9
more than 80% of maximal activity is obtained between pH 7.8 and 9.0, at 25°C, which corresponds to pH 6.5-7.7 at 72°C when Tris is used as a buffer
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25
30
37
42
50
60
65
65 - 70
70
70 - 75
72
72 - 76
maximal DNA polymerase activity is observed between 72 and 76°C, above which activity decreases abruptly
73
-
optimal temperature for an equimolar dNTP pool is 72.5°C. The optimum temperature shifts to lower temperatures when the dNTP pool composition is biased
75
additional information
70
-
the replication fidelity of the enzyme is about three times as high at 70°C as at 55°C
70 - 75
recombinant enzyme with the nonspecific DNA-binding protein Sso7d from Sulfolobus solfataricus fused to the C-terminus
additional information
the optimal temperature for polymerase activity could not be measured because activated DNA is not stable above 75°C
additional information
the optimal temperature for polymerase activity could not be measured because activated DNA is not stable above 75°C
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
2 - 80
-
the incorporation rate for correct nucleotides increases by 18900fold from 2°C to 56°C, the fidelity of Dpo4 at 80°C is similar to that determined at 56°C
22 - 72
-
activity range, the error frequency of the enzyme does not change significantly when the temperature is raised from 22°C to 72°C
25 - 60
25 - 70
27 - 55
27°C: about 50% of maximal activity, 55°C: about 35% of maximal activity, activity with activated calf thymus DNA
37 - 55
37 - 65
55 - 80
-
55°C: about 45% of maximal activity, 80°C: about 45% of maximal activity, substrate activated calf-thymus DNA
60 - 80
60°C: about 45% of maximal activity, 80°C: about 50% of maximal activity, recombinant enzyme with the nonspecific DNA-binding protein Sso7d from Sulfolobus solfataricus fused to the C-terminus
60 - 85
60°C: about 65% of maximal activity, 85°C: about 75% of maximal activity
60 - 90
60°C: about 45% of maximal activity, 90°C: about 40% of maximal activity, calf thymus DNA template
65 - 80
65°C: about 60% of maximal activity, 80°C: about 60% of maximal activity
65 - 85
-
65°C: about 70% of maximal activity, 85°C: about 50% of maximal activity
65 - 90
-
65°C: about 40% of maximal activity, 90°C: about 50% of maximal activity
70 - 75
-
optimal RNAse H activity at 70°C, sharp decline of activity above 75°C
70 - 85
70°C: about 55% of maximal activity, 85°C: about 70% of maximal activity
25 - 60
the catalytic activities of DNA polymerase Dpo2 gradually increases from 25 to 50°C but abruptly decreases at 60°C, at which it is only20% of the activity at 50°C (and even lower than the activities at 37°C) and is abolished at 70 °C
25 - 60
the catalytic activity of DNA polymerase Dpo3 gradually increases from 25 to 50°C but abruptly decreases at 60°C, at which it is 20% of the activity at 50°C (and even lower than the activity at 37°C) and is abolished at 70°C
25 - 70
activities of DNA polymerase Dpo1 gradually increases from 25 to 60°C and is substantial even at 70°C, with40% of the activity at 60°C
25 - 70
activity of DNA polymerase Dpo4 gradually increases from 25 to 60°C and is substantial even at 70°C, with60% of the activity at 60°C
37 - 65
activity at 65°C (optimum) is 20fold higher than at 37°C. A rapid 10fold increase occurs at 70-80°C
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.6
-
2 species with pI 7.6 and pI 8, twodimensional electrophoresis, 1st dimension: isoelectric focusing, pH gradient between pH 3.5 and 10, 2nd dimension: SDS-PAGE
8
-
2 species with pI 7.6 and pI 8, twodimensional electrophoresis, 1st dimension: isoelectric focusing, pH gradient between pH 3.5 and 10, 2nd dimension: SDS-PAGE
9.1
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
isolated from hot springs in Gönen and Hisaralan, Turkey, gene polA
UniProt
brenda
isolated from hot springs in Gönen and Hisaralan, Turkey, gene polA
UniProt
brenda
Herpes simplex virus
gene MIP1 encoding DNA pol gamma, and gene POL1 encoding DNA polymerase alpha catalytic subunit A
UniProt
brenda
Thermus aquaticus INValphaF''
Escherichia coli transformed with the pTaq plasmid containing the Taq gene expressed under control of the tac promoter
-
-
brenda
5 cellular DNA template-dependent DNA polymerases are encoded by distinct genes: polymerase alpha, i.e. pol I, polymerase beta, only in vertebrates, polymerase gamma, required for mitochondrial DNA replication but encoded in the nucleus, polymerase delta, enzymes in mammalian cell contain tightly associated 3'-5'-exonuclease activities, 2 forms: proliferating cell nuclear antigen-dependent and a proliferating cell nuclear antigen-independent, also called DNA polymerase delta II, now named DNA polymerase epsilon, polymerase epsilon, tightly associated 3'-5'-exonuclease activity, formerly named DNA polymerase delta II
-
-
brenda
-
643594, 643602, 643608, 643609, 643622, 643649, 643650, 643655, 643668, 691213, 691631, 692423, 692685
-
-
brenda
5 cellular DNA template-dependent DNA polymerases are encoded by distinct genes: polymerase alpha, i.e. pol I, polymerase beta, only in vertebrates, polymerase gamma, required for mitochondrial DNA replication but encoded in the nucleus, polymerase delta, enzymes in mammalian cell contain tightly associated 3'-5'-exonuclease activities, 2 forms: proliferating cell nuclear antigen-dependent and a proliferating cell nuclear antigen-independent, also called DNA polymerase delta II, now named DNA polymerase epsilon, polymerase epsilon, tightly associated 3'-5'-exonuclease activity, formerly named DNA polymerase delta II
-
-
brenda
-
-
-
brenda
5 cellular DNA template-dependent DNA polymerases are encoded by distinct genes: polymerase alpha, i.e. pol I, polymerase beta, only in vertebrates, polymerase gamma, required for mitochondrial DNA replication but encoded in the nucleus, polymerase delta, enzymes in mammalian cell contain tightly associated 3'-5'-exonuclease activities, 2 forms: proliferating cell nuclear antigen-dependent and a proliferating cell nuclear antigen-independent, also called DNA polymerase delta II, now named DNA polymerase epsilon, polymerase epsilon, tightly associated 3'-5'-exonuclease activity, formerly named DNA polymerase delta II
-
-
brenda
-
-
-
brenda
5 cellular DNA template-dependent DNA polymerases are encoded by distinct genes: polymerase alpha, i.e. pol I, polymerase beta, only in vertebrates, polymerase gamma, required for mitochondrial DNA replication but encoded in the nucleus, polymerase delta, enzymes in mammalian cell contain tightly associated 3'-5'-exonuclease activities, 2 forms: proliferating cell nuclear antigen-dependent and a proliferating cell nuclear antigen-independent, also called DNA polymerase delta II, now named DNA polymerase epsilon, polymerase epsilon, tightly associated 3'-5'-exonuclease activity, formerly named DNA polymerase delta II
-
-
brenda
-
-
-
brenda
-
673942, 674540, 674697, 674850, 675228, 675808, 675966, 676223, 676226, 691213, 691631, 692423, 692685, 693396, 693630, 701733, 702026, 702071, 702087
-
-
brenda
5 cellular DNA template-dependent DNA polymerases are encoded by distinct genes: polymerase alpha, i.e. pol I, polymerase beta, only in vertebrates, polymerase gamma, required for mitochondrial DNA replication but encoded in the nucleus, polymerase delta, enzymes in mammalian cell contain tightly associated 3'-5'-exonuclease activities, 2 forms: proliferating cell nuclear antigen-dependent and a proliferating cell nuclear antigen-independent, also called DNA polymerase delta II, now named DNA polymerase epsilon, polymerase epsilon, tightly associated 3'-5'-exonuclease activity, formerly named DNA polymerase delta II
-
-
brenda
Q07864: catalytic subunit A, Q9NR33: subunit 4, P56282: subunit 2, Q9NRF9: subunit 3
SwissProt
brenda
mouse strains defective in specialized DNA polymerases are used for studying their function
-
-
brenda
two family Y DNA polymerases Rv1537 and Rv3056
UniProt
brenda
small subunit polB: Q9V2F3, large subunit polC: Q9V2F4
SwissProt
brenda
P81412: DP1, small subunit. P81409: DP2, large subunit
SwissProt
brenda
O57863: DNA polymerase II small subunit, gene name polB, ordered locus name: PH0123, O57861: DNA polymerase II large subunit, gene name polC, ordered locus name: PH0121
-
brenda
O57863: DNA polymerase II small subunit, gene name polB, ordered locus name: PH0123, O57861: DNA polymerase II large subunit, gene name polC, ordered locus name: PH0121
-
brenda
-
643594, 643611, 643613, 643624, 643628, 643649, 671793, 672254, 691213, 691631, 692423, 692685, 702387, 721656
-
-
brenda
5 cellular DNA template-dependent DNA polymerases are encoded by distinct genes: polymerase alpha, i.e. pol I, polymerase beta, only in vertebrates, polymerase gamma, required for mitochondrial DNA replication but encoded in the nucleus, polymerase delta. Enzymes in mammalian cell contain tightly associated 3'-5'-exonuclease activities, 2 forms: proliferating cell nuclear antigen-dependent and a proliferating cell nuclear antigen-independent polymerase, also called DNA polymerase delta II, now named DNA polymerase epsilon, polymerase epsilon, tightly associated 3'-5'-exonuclease activity, formerly named DNA polymerase delta II
-
-
brenda
-
UniProt
brenda
-
UniProt
brenda
-
643607, 643608, 643625, 643649, 643650, 643664, 643666, 662368, 674684, 675808, 676222, 703451, 704568
-
-
brenda
gene MIP1 encoding DNA pol gamma, and gene POL1 encoding DNA polymerase alpha catalytic subunit A
UniProt
brenda
Escherichia coli transformed with the pTaq plasmid containing the Taq gene expressed under control of the tac promoter
-
-
brenda
group C adenovirus 5 and group B adenovirus 35 ATCC prototype strains
-
-
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
-
Trypanosoma cruzi DNA polymerase beta is restricted to the antipodal sites of kDNA in replicative epimastigote and amastigote developmental stages, being strictly localized to kDNA antipodal sites between G1/S and early G2 phase in replicative epimastigotes
brenda
-
Trypanosoma cruzi DNA polymerase beta is restricted to the antipodal sites of kDNA in replicative epimastigote and amastigote developmental stages, being strictly localized to kDNA antipodal sites between G1/S and early G2 phase in replicative epimastigotes
brenda
-
-
brenda
-
enzyme is active only in cells at meiotic prophase, in somatic cells it is in an inactive state
brenda
-
-
brenda
additional information
additional information
human DNA polymerase eta expression is detected in most tissues except for very low or undetectable levels in peripheral lymphocytes, fetal spleen, and adult muscle
brenda
additional information
-
human DNA polymerase eta expression is detected in most tissues except for very low or undetectable levels in peripheral lymphocytes, fetal spleen, and adult muscle
brenda
additional information
-
highly expressed both in proliferative and non-proliferative developmental forms
brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
Trypanosoma cruzi DNA polymerase beta is restricted to the antipodal sites of kDNA in replicative epimastigote and amastigote developmental stages, being strictly localized to kDNA antipodal sites between G1/S and early G2 phase in replicative epimastigotes
brenda
additional information
in yeast mitochondria two different DNA polymerases exist, pol gamma and pol NI, i.e. DNA polymerase alpha catalytic subunit A and its associated DNA polymerase subunit alphabeta, POL12
brenda
-
in yeast mitochondria two different DNA polymerases exist, pol gamma and pol NI, i.e. DNA polymerase alpha catalytic subunit A and its associated DNA polymerase subunit alphabeta, POL12
-
brenda
additional information
-
bacteriophage PRD1 enzyme overexpressed in Escherichia coli has a soluble and an insoluble activity indistinguishable by enzymatic properties
-
brenda
additional information
-
DNA polymerase beta localizes to the synaptonemal complex during prophase I of meiosis, the enzyme localizes to synapsed axes during zygonema and pachynema, and it associates with the ends of bivalents during late pachynema and diplonema
-
brenda
additional information
-
subcellular localization of Tcpolbeta is restricted to antipodal sites in replicating cells, while in nonreplicative cultured trypomastigotes Tcpolbeta is dispersed inside its single ramified mitochondrion. The subcellular localization of Tcpolbeta follows the parasite cell cycle, overview
-
brenda
Highest Expressing Human Cell Lines
Cell Line LinksPlease wait a moment until the data is sorted. This message will disappear when the data is sorted.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug target
evolution
malfunction
metabolism
physiological function
additional information
drug target
R61 and S62 play key roles in the specificity and effectiveness of DNA polymerase eta for bypassing TTD lesions during DNA replication. Understanding the basis for this specificity is important for designing drugs aimed at cancer treatment
drug target
the enzyme is an attractive target for cancer therapies because it has been correlated with a shorter survival time in patients with glioblastoma as well as poor chemotherapy responses in some cases
evolution
-
human DNA polymerase lambda is a member of the DNA polymerase X family
evolution
DNA polymerase I belongs to the DNA polymerase family A, all the functionally important regions in the polymerase active site of Geobacillus kaue polI are conserved, phylogenetic analysis, evolutionary relationship of diverse Geobacillus species, overview
evolution
K4PolI is a family A DNA polymerase, phylogenetic tree
evolution
-
the enzyme belongs to the DNA polymerase Y-family, phylogenetic analysis
evolution
compared to mammalian pol betas, the Danio rerio enzyme contains a P63D amino acid substitution. This substitution lies in a hairpin sequence within an 8-kDa domain, likely to be important in DNA binding
evolution
-
the catalytic subunits Pol1, Pol2 and Pol3 or isozymes pol alpha, pol epsilon, and pol delta are phylogenetically related, and belong to the class B DNA polymerases. The B subunits are all essential and share a phosphodiesterase-like and oligosaccharide binding domain. Eukaryotes contain a fourth class B DNA polymerase, Pol zeta, which is the major enzyme responsible for mutagenesis in response to DNA damage
evolution
a self-activated mechanism for efficient polymerase catalysis is proposed, which is based on the identification of an evolutionary convergence to preserve a key enzymatic structural element in all the available X-ray structures of DNA/RNA polymerases from all domains of life
evolution
-
the catalytic subunits Pol1, Pol2 and Pol3 or isozymes pol alpha, pol epsilon, and pol delta are phylogenetically related, and belong to the class B DNA polymerases. The B subunits are all essential and share a phosphodiesterase-like and oligosaccharide binding domain. Eukaryotes contain a fourth class B DNA polymerase, Pol zeta, which is the major enzyme responsible for mutagenesis in response to DNA damage
-
evolution
-
DNA polymerase I belongs to the DNA polymerase family A, all the functionally important regions in the polymerase active site of Geobacillus kaue polI are conserved, phylogenetic analysis, evolutionary relationship of diverse Geobacillus species, overview
-
malfunction
-
class switch recombination is normal in mice deficient for pols theta and eta
malfunction
-
cell lines downregulating poliota exhibit hypersensitivity to DNA damage induced by hydrogen peroxide or menadione but not to ethylmethane sulfonate, UVC or UVA, extracts from cells downregulating poliota show reduced base excision repair activity
malfunction
-
Pol beta-deficient spermatocytes are defective in meiotic chromosome synapsis and undergo apoptosis during prophase I, Pol beta-deficient seminferous tubules have few germ cells, Pol beta-deficient spermatocytes do not progress through meiosis, Pol beta-deficient mice are fertile
malfunction
-
the depletion of Pol eta or Pol kappa elevates DNA damage associated with non-plasmid pULCtrl formed at the human c-MYC promoter
malfunction
-
depletion of Pol eta from undamaged human cells affects cell cycle progression (G2/M and proliferative defects) and the rate of cell proliferation and results in increased spontaneous chromosome breaks and common fragile site expression with the activation of ATM-mediated DNA damage checkpoint signaling
malfunction
-
mutations in or altered expression of Pol gamma coupled with oxidative damage to mitochondrial DNA may be involved in Parkinson disease and Alzheimer disease
malfunction
-
abo4 mutants show early flowering and reduced expression of flowering locus C and increased expression of flowering locus T with changing histone H3 modifications
malfunction
DNA polymerase eta-deficient cells show strong activation of downstream DNA damage responses including ataxia-telangiectasia mutated and Rad3-related protein signaling and accumulate strand breaks as result of replication fork collapse
malfunction
-
abolished catalytic activity of mutant enzyme in the presence of two metal ions, Mg2+ and Mn2+, overview
malfunction
-
enhanced fidelity of base selection by a polymerase active site can result in impaired lesion bypass and delayed replication fork progression
malfunction
-
more than 150 different point mutations in POLG, the gene encoding the human mitochondrial DNA polymerase gamma, cause a broad spectrum of childhood and adult onset diseases. Disorders associated with POLG mutations include: 1. myocerebrohepatopathy spectrum disorder 2. Alpers syndrome 3. ataxia neuropathy spectrum disorder 4. myoclonus epilepsy myopathy sensory ataxia 5. autosomal recessive progressive external ophthalmoplegia 6. autosomal dominant progressive external ophthalmoplegia. Also, alteration of the (CAG)10 repeat in the 2nd exon of POLG is implicated in male infertility
malfunction
-
silencing of each polymerase, of mitochondrial DNA polymerases IB, IC, and ID, is lethal, resulting in kDNA loss, persistence of prereplication DNA monomers, and collapse of the mitochondrial membrane potential. Kinetics of kDNA loss during DNA polymerase silencing, overview
malfunction
-
weakened Fe-S cluster binding efficiency of CysA mutant proteins, caused by a lack of polymerase complex stabilization by Pol31, even though this subunit interacts primarily with the CysB region, overexpression of Pol31 results in a 4 to 8fold higher 55Fe binding to both wild-type and CysA mutant Pol3-CTDs. Depletion of the cysteine desulfurase Nfs1 by growth on glucose of the galactose-regulatable strain Gal-NFS1 almost completely abolishes Fe binding to the polymerases, and depletion of the CIA machinery components Nbp35 and Nar1 in regulatable yeast strains abrogates Fe-S cluster formation on the polymerases
malfunction
many cancer-associated single-nucleotide polymorphisms have been reported in the Pol kappa gene, some of which are associated with poor survival and altered chemotherapy response
malfunction
-
weakened Fe-S cluster binding efficiency of CysA mutant proteins, caused by a lack of polymerase complex stabilization by Pol31, even though this subunit interacts primarily with the CysB region, overexpression of Pol31 results in a 4 to 8fold higher 55Fe binding to both wild-type and CysA mutant Pol3-CTDs. Depletion of the cysteine desulfurase Nfs1 by growth on glucose of the galactose-regulatable strain Gal-NFS1 almost completely abolishes Fe binding to the polymerases, and depletion of the CIA machinery components Nbp35 and Nar1 in regulatable yeast strains abrogates Fe-S cluster formation on the polymerases
-
metabolism
-
high levels of DNA polymerases of the X family might cause genomic instability
metabolism
-
the pol gamma holoenzyme functions in conjunction with the mitochondrial DNA helicase and the mitochondrial SSB to form the minimal replication apparatus
metabolism
DNA replication can be accomplished using dNDPs as substrates. In thermophiles, genome replication may be less sensitive to the energy charge of the cell than in mesophiles because thermostable polymerases can accept the diphosphorylated as well as the triphosphorylated substrates. DNA replication is thus less affected by the intracellular ATP/ADP ratio, and the relatively high efficiency with which DNA is synthesized at elevated temperatures suggests that thermophiles may be able to dispense with the triphosphorylated substrates entirely
metabolism
DNA replication can be accomplished using dNDPs as substrates. In thermophiles, genome replication may be less sensitive to the energy charge of the cell than in mesophiles because thermostable polymerases can accept the diphosphorylated as well as the triphosphorylated substrates. DNA replication is thus less affected by the intracellular ATP/ADP ratio, and the relatively high efficiency with which DNA is synthesized at elevated temperatures suggests that thermophiles may be able to dispense with the triphosphorylated substrates entirely
metabolism
DNA replication can be accomplished using dNDPs as substrates. In thermophiles, genome replication may be less sensitive to the energy charge of the cell than in mesophiles because thermostable polymerases can accept the diphosphorylated as well as the triphosphorylated substrates. DNA replication is thus less affected by the intracellular ATP/ADP ratio, and the relatively high efficiency with which DNA is synthesized at elevated temperatures suggests that thermophiles may be able to dispense with the triphosphorylated substrates entirely
metabolism
DNA replication can be accomplished using dNDPs as substrates. In thermophiles, genome replication may be less sensitive to the energy charge of the cell than in mesophiles because thermostable polymerases can accept the diphosphorylated as well as the triphosphorylated substrates. DNA replication is thus less affected by the intracellular ATP/ADP ratio, and the relatively high efficiency with which DNA is synthesized at elevated temperatures suggests that thermophiles may be able to dispense with the triphosphorylated substrates entirely
physiological function
-
Poleta may be involved in induction of various types of mutations through the erroneous and efficient incorporation of oxidized dNTPs into DNA
physiological function
-
pol theta has no major involvement in somatic hypermutation
physiological function
-
Pol beta is a DNA polymerase specific to base excision repair that also possesses lyase activity capable of severing the phosphoester bond on the 3' carbon of the abasic ribose
physiological function
poliota uniquely replicates DNA with a constrained active site, creating shorter C1'-C1' strand distances, with the finger domain projecting the template base out towards the solvent-accessible major groove and stabilizing a mismatched G base through H-bonding
physiological function
-
human poliota protects cells from oxidative damage, poliota binds to chromatin after oxidative damage
physiological function
-
DNA polymerase epsilon and the histone H3 acetylase, Rtt109, are required for the formation/maintenance of this histone-depleted region and for the recruitment of the transcription factors to the tRNA
physiological function
-
DNA polymerase beta is critical for mouse meiotic synapsis, Pol beta is required at a very early step in the processing of meiotic double-strand breaks, at or before the removal of SPO11 from double-strand break ends and the generation of the 3' single-stranded tails necessary for subsequent strand exchange
physiological function
-
Trypanosoma cruzi overexpressing Poleta is more resistant to treatment with hydrogen peroxide compared to nontransfected cells, does not increase its resistance to UV-light (with or without caffeine) or cisplatin, and is also unable to restore growth after treatment with zeocin or gamma irradiation
physiological function
-
DNA polymerase eta is a limiting factor for A:T mutations in immunglobulin genes and contributes to antibody affinity maturation in germinal center B cells
physiological function
the presence of 5'->3' exonuclease activity in DNA polymerase can replace mismatched base pairs with the correct nucleotide, DNA polymerase possesses 3'->5' exonuclease activity
physiological function
-
POLD4 is required for the in vitro pol delta activity, and functions in cell proliferation and maintenance of genomic stability of human cells
physiological function
-
phi29 DNA polymerase is fully responsible for viral DNA replication
physiological function
-
DNA polymerase epsilon with 3'-5' proofreading exonuclease activity bypasses only the model abasic site during processive synthesis and cannot reinitiate DNA synthesis
physiological function
-
the interaction between DNA polymerase eta and MLH1 is involved in DNA replication, MutSalpha can interact with Poleta through MutLalpha
physiological function
-
polymerase alpha (p70-p180 or p49-p58-p70-p180 complex) extends herpes primase-synthesized RNA primers much more efficiently than herpes polymerase
physiological function
-
involvement of deinococcal polymerase X in DNA-damage tolerance, possibly by contributing to DNA double-strand break repair and base excision repair
physiological function
-
both Pol eta and Pol kappa prevent genomic instability occurring at natural DNA sequences capable of forming unusual secondary structures in human cells
physiological function
-
human DNA polymerase eta modulates susceptibility to skin cancer by promoting translesion DNA synthesis past sunlight-induced cyclobutane pyrimidine dimers
physiological function
-
Polkappa efficiently bypasses 8-oxoguanine lesions, Polkappa increases Trypanosoma cruzi resistance to high doses of gamma irradiation and zeocin and can catalyse DNA synthesis within recombination intermediates
physiological function
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DNA polymerases have abortive DNA synthesis upon encountering apurinic/apyrimidinic sites. Under running start conditions, polB can incorporate in front of the damage and even replicate to the full-length oligonucleotides containing a specific apurinic/apyrimidinic site, but only when present at a molar excess. Conversely, bypassing activity of polD is strictly inhibited
physiological function
-
Pol alpha catalyses initiation of chromosomal DNA replication at origins and at Okazaki fragments on the lagging strand, Pol beta participates in base-excision repair, Pol gamma catalyses mitochondrial DNA synthetic processes, Pol delta participates in lagging-strand synthesis, and Pol epsilon has a role in the synthesis of the leading strand of chromosomal DNA, Pol eta functions in bypass UV lesions,Pol iota, Pol kappa, and Pol zeta function in bypass synthesis, Pol lambda functions in base excision repair, Pol mu functions in non-homologous end joining, Pol theta functions in DNA repair, and DNA polymerase Rec1 incorporates dC opposite abasic sites. Pol beta can be classified as a tumour suppressor
physiological function
-
DNA polymerase eta confers UV resistance by catalyzing translesion synthesis past UV photoproducts
physiological function
DNA polymerase eta is a key protein in translesion synthesis in human cells, it is a low-fidelity enzyme when copying undamaged DNA but can carry out error-free translesion synthesis at sites of UV-induced dithymine cyclobutane pyrimidine dimmers. DNA polymerase eta plays an important role in preventing genome instability after UV- and cisplatin-induced DNA damage
physiological function
DNA polymerase iota is also capable of error-free nucleotide incorporation opposite the bulky major groove adduct N-(deoxyguanosin-8-yl)-2-acetyl-aminofluorene
physiological function
Dbh DNA polymerase has multiple functions affecting the stability of the Sulfolobus genome, suppressing certain mutations at particular sites and promoting other mutations elsewhere
physiological function
Dpo3 is a potential player in the proper maintenance of the archaeal genome
physiological function
-
three eukaryotic DNA replicative polymerases, Pol alpha, Pol delta, and Pol epsilon, are involved in chromosomal DNA replication. RNA/DNA primers synthesized by Pol alpha/primase are elongated by Pol delta and/or Pol epsilon. Pol delta requires the DNA sliding clamp, proliferating cell nuclear antigen, PCNA, for highly processive enzyme activity
physiological function
-
DNA Pol lambda has a backup role for DNA Pol beta in base-excision repair
physiological function
error-prone DNA polymerases belonging to the Y-family in mycobacteria do not participate in adaptive mutagenesis, in contrast to the representatives of theis faamily in other prokaryotes. Escherichia coli gene dinB homologues in mycobacteria code for nonfunctional molecules that are devoid of enzyme activity
physiological function
-
most damage-induced mutagenesis in Escherichia coli is dependent on pol V Pol V has intrinsically weak DNA polymerase activity, but its catalytic activity can be stimulated in vitro in the presence the beta-processivity clamp, RecA protein bound to ssDNA, and single-stranded-binding (SSB) protein. Processivity of pol V in the presence of accessory factors, overview
physiological function
-
pol gamma is absolutely essential for mitochondrial DNA replication and repair
physiological function
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DNA polymerase beta from Trypanosoma cruzi is involved in kinetoplast DNA replication and repair of oxidative lesions, Tcpolbeta is involved in oxidative stress response, Tcpolbeta overexpression improves epimastigote survival in presence of H2O2
physiological function
-
DNA polymerase III, an enzyme complex consisting of ten subunits, is responsible for genome duplication
physiological function
-
the enzyme plays an essential role in DNA replication, repair, and recombination
physiological function
-
the parasite's single mitochondrion contains a unique catenated mitochondrial DNA network called kinetoplast DNA (kDNA) that is composed of minicircles and maxicircles. Three kDNA replication proteins (mitochondrial DNA polymerases IB, IC, and ID) are required for bloodstream form parasite viability
physiological function
-
the DNA polymerase catalyzes efficient and accurate translesion synthesis past cis-syn cyclobutane pyrimidine dimers, as well as 7,8-dihydro-8-oxoguanine and isomers of thymine glycol induced by reactive oxygen species
physiological function
-
the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis
physiological function
-
DNA damage that eludes cellular repair pathways can arrest the replication machinery and stall the cell cycle. This damage can be bypassed by the Y-family DNA polymerases
physiological function
the template-dependent polymerase that can repair non-complementary DNA double strand breaks with unpaired 3' primer termini by nonhomologous end joining. Its role is to fill short gaps arising as intermediates in the process of V(D)J recombination and during processing of accidental double strand breaks
physiological function
-
in translesion synthesis (TLS), specialized DNA polymerases, such as polymerase (pol) eta, are recruited to stalled replication forks. The polymerase form a multi-protein complex with PCNA, Rad6-Rad18, and other specialized polymerases. Pol eta interacts with PCNA and Rev1 via a PCNA-interacting protein (PIP) motif in its C-terminal unstructured region. PIP1 likely plays a critical role in the recruiting pol eta to the multi-protein complex. PIP2 likely plays a critical role in maintaining the architecture and the dynamics of this multi-protein complex needed to maximize the efficiency and accuracy of translesion synthesis
physiological function
DNA polymerase epsilon (Pole) is responsible for leading strand synthesis. The presence of the C-terminal domain of the catalytic subunit (p261C) and the three small subunits regulates the 3'->5' exonuclease activity of the hPole holoenzyme. Together, the 3'->5 exonuclease activity and the variable mismatch extension activity modulate the overall fidelity of the hPole holoenzyme by up to 3 orders of magnitude. The presence of p261C and the three noncatalytic subunits optimizes the dual enzymatic activities of the catalytic p261 subunit and makes the hPole holoenzyme an efficient and faithful replicative DNA polymerase
physiological function
DNA polymerase eta plays a vital role in protection against skin cancer caused by damage from ultraviolet light. The enzyme rescues stalled replication forks at cyclobutane thymine-thymine dimers (TTDs) by inserting nucleotides opposite these DNA lesions
physiological function
the enzyme has roles both in maintaining and compromising genomic integrity. The expression of pol kappa is altered in several different cancer types, which can lead to genome instability
physiological function
in translesion synthesis (TLS), specialized DNA polymerases, such as polymerase (pol) eta, are recruited to stalled replication forks. The polymerase form a multi-protein complex with PCNA, Rad6-Rad18, and other specialized polymerases. Pol eta interacts with PCNA and Rev1 via a PCNA-interacting protein (PIP) motif in its C-terminal unstructured region. PIP1 likely plays a critical role in the recruiting pol eta to the multi-protein complex. PIP2 likely plays a critical role in maintaining the architecture and the dynamics of this multi-protein complex needed to maximize the efficiency and accuracy of translesion synthesis
physiological function
-
in translesion synthesis (TLS), specialized DNA polymerases, such as polymerase (pol) eta, are recruited to stalled replication forks. The polymerase form a multi-protein complex with PCNA, Rad6-Rad18, and other specialized polymerases. Pol eta interacts with PCNA and Rev1 via a PCNA-interacting protein (PIP) motif in its C-terminal unstructured region. PIP1 likely plays a critical role in the recruiting pol eta to the multi-protein complex. PIP2 likely plays a critical role in maintaining the architecture and the dynamics of this multi-protein complex needed to maximize the efficiency and accuracy of translesion synthesis
physiological function
-
in translesion synthesis (TLS), specialized DNA polymerases, such as polymerase (pol) eta, are recruited to stalled replication forks. The polymerase form a multi-protein complex with PCNA, Rad6-Rad18, and other specialized polymerases. Pol eta interacts with PCNA and Rev1 via a PCNA-interacting protein (PIP) motif in its C-terminal unstructured region. PIP1 likely plays a critical role in the recruiting pol eta to the multi-protein complex. PIP2 likely plays a critical role in maintaining the architecture and the dynamics of this multi-protein complex needed to maximize the efficiency and accuracy of translesion synthesis
physiological function
-
in translesion synthesis (TLS), specialized DNA polymerases, such as polymerase (pol) eta, are recruited to stalled replication forks. The polymerase form a multi-protein complex with PCNA, Rad6-Rad18, and other specialized polymerases. Pol eta interacts with PCNA and Rev1 via a PCNA-interacting protein (PIP) motif in its C-terminal unstructured region. PIP1 likely plays a critical role in the recruiting pol eta to the multi-protein complex. PIP2 likely plays a critical role in maintaining the architecture and the dynamics of this multi-protein complex needed to maximize the efficiency and accuracy of translesion synthesis
physiological function
-
in translesion synthesis (TLS), specialized DNA polymerases, such as polymerase (pol) eta, are recruited to stalled replication forks. The polymerase form a multi-protein complex with PCNA, Rad6-Rad18, and other specialized polymerases. Pol eta interacts with PCNA and Rev1 via a PCNA-interacting protein (PIP) motif in its C-terminal unstructured region. PIP1 likely plays a critical role in the recruiting pol eta to the multi-protein complex. PIP2 likely plays a critical role in maintaining the architecture and the dynamics of this multi-protein complex needed to maximize the efficiency and accuracy of translesion synthesis
physiological function
-
in translesion synthesis (TLS), specialized DNA polymerases, such as polymerase (pol) eta, are recruited to stalled replication forks. The polymerase form a multi-protein complex with PCNA, Rad6-Rad18, and other specialized polymerases. Pol eta interacts with PCNA and Rev1 via a PCNA-interacting protein (PIP) motif in its C-terminal unstructured region. PIP1 likely plays a critical role in the recruiting pol eta to the multi-protein complex. PIP2 likely plays a critical role in maintaining the architecture and the dynamics of this multi-protein complex needed to maximize the efficiency and accuracy of translesion synthesis
physiological function
-
in translesion synthesis (TLS), specialized DNA polymerases, such as polymerase (pol) eta, are recruited to stalled replication forks. The polymerase form a multi-protein complex with PCNA, Rad6-Rad18, and other specialized polymerases. Pol eta interacts with PCNA and Rev1 via a PCNA-interacting protein (PIP) motif in its C-terminal unstructured region. PIP1 likely plays a critical role in the recruiting pol eta to the multi-protein complex. PIP2 likely plays a critical role in maintaining the architecture and the dynamics of this multi-protein complex needed to maximize the efficiency and accuracy of translesion synthesis
physiological function
in translesion synthesis (TLS), specialized DNA polymerases, such as polymerase (pol) eta, are recruited to stalled replication forks. The polymerase form a multi-protein complex with PCNA, Rad6-Rad18, and other specialized polymerases. Pol eta interacts with PCNA and Rev1 via a PCNA-interacting protein (PIP) motif in its C-terminal unstructured region. PIP1 likely plays a critical role in the recruiting pol eta to the multi-protein complex. PIP2 likely plays a critical role in maintaining the architecture and the dynamics of this multi-protein complex needed to maximize the efficiency and accuracy of translesion synthesis
physiological function
-
in translesion synthesis (TLS), specialized DNA polymerases, such as polymerase (pol) eta, are recruited to stalled replication forks. The polymerase form a multi-protein complex with PCNA, Rad6-Rad18, and other specialized polymerases. Pol eta interacts with PCNA and Rev1 via a PCNA-interacting protein (PIP) motif in its C-terminal unstructured region. PIP1 likely plays a critical role in the recruiting pol eta to the multi-protein complex. PIP2 likely plays a critical role in maintaining the architecture and the dynamics of this multi-protein complex needed to maximize the efficiency and accuracy of translesion synthesis
physiological function
-
in translesion synthesis (TLS), specialized DNA polymerases, such as polymerase (pol) eta, are recruited to stalled replication forks. The polymerase form a multi-protein complex with PCNA, Rad6-Rad18, and other specialized polymerases. Pol eta interacts with PCNA and Rev1 via a PCNA-interacting protein (PIP) motif in its C-terminal unstructured region. PIP1 likely plays a critical role in the recruiting pol eta to the multi-protein complex. PIP2 likely plays a critical role in maintaining the architecture and the dynamics of this multi-protein complex needed to maximize the efficiency and accuracy of translesion synthesis
physiological function
-
in translesion synthesis (TLS), specialized DNA polymerases, such as polymerase (pol) eta, are recruited to stalled replication forks. The polymerase form a multi-protein complex with PCNA, Rad6-Rad18, and other specialized polymerases. Pol eta interacts with PCNA and Rev1 via a PCNA-interacting protein (PIP) motif in its C-terminal unstructured region. PIP1 likely plays a critical role in the recruiting pol eta to the multi-protein complex. PIP2 likely plays a critical role in maintaining the architecture and the dynamics of this multi-protein complex needed to maximize the efficiency and accuracy of translesion synthesis
physiological function
-
in translesion synthesis (TLS), specialized DNA polymerases, such as polymerase (pol) eta, are recruited to stalled replication forks. The polymerase form a multi-protein complex with PCNA, Rad6-Rad18, and other specialized polymerases. Pol eta interacts with PCNA and Rev1 via a PCNA-interacting protein (PIP) motif in its C-terminal unstructured region. PIP1 likely plays a critical role in the recruiting pol eta to the multi-protein complex. PIP2 likely plays a critical role in maintaining the architecture and the dynamics of this multi-protein complex needed to maximize the efficiency and accuracy of translesion synthesis
physiological function
-
in translesion synthesis (TLS), specialized DNA polymerases, such as polymerase (pol) eta, are recruited to stalled replication forks. The polymerase form a multi-protein complex with PCNA, Rad6-Rad18, and other specialized polymerases. Pol eta interacts with PCNA and Rev1 via a PCNA-interacting protein (PIP) motif in its C-terminal unstructured region. PIP1 likely plays a critical role in the recruiting pol eta to the multi-protein complex. PIP2 likely plays a critical role in maintaining the architecture and the dynamics of this multi-protein complex needed to maximize the efficiency and accuracy of translesion synthesis
physiological function
-
in translesion synthesis (TLS), specialized DNA polymerases, such as polymerase (pol) eta, are recruited to stalled replication forks. The polymerase form a multi-protein complex with PCNA, Rad6-Rad18, and other specialized polymerases. Pol eta interacts with PCNA and Rev1 via a PCNA-interacting protein (PIP) motif in its C-terminal unstructured region. PIP1 likely plays a critical role in the recruiting pol eta to the multi-protein complex. PIP2 likely plays a critical role in maintaining the architecture and the dynamics of this multi-protein complex needed to maximize the efficiency and accuracy of translesion synthesis
physiological function
-
in translesion synthesis (TLS), specialized DNA polymerases, such as polymerase (pol) eta, are recruited to stalled replication forks. The polymerase form a multi-protein complex with PCNA, Rad6-Rad18, and other specialized polymerases. Pol eta interacts with PCNA and Rev1 via a PCNA-interacting protein (PIP) motif in its C-terminal unstructured region. PIP1 likely plays a critical role in the recruiting pol eta to the multi-protein complex. PIP2 likely plays a critical role in maintaining the architecture and the dynamics of this multi-protein complex needed to maximize the efficiency and accuracy of translesion synthesis
physiological function
-
in translesion synthesis (TLS), specialized DNA polymerases, such as polymerase (pol) eta, are recruited to stalled replication forks. The polymerase form a multi-protein complex with PCNA, Rad6-Rad18, and other specialized polymerases. Pol eta interacts with PCNA and Rev1 via a PCNA-interacting protein (PIP) motif in its C-terminal unstructured region. PIP1 likely plays a critical role in the recruiting pol eta to the multi-protein complex. PIP2 likely plays a critical role in maintaining the architecture and the dynamics of this multi-protein complex needed to maximize the efficiency and accuracy of translesion synthesis
physiological function
-
in translesion synthesis (TLS), specialized DNA polymerases, such as polymerase (pol) eta, are recruited to stalled replication forks. The polymerase form a multi-protein complex with PCNA, Rad6-Rad18, and other specialized polymerases. Pol eta interacts with PCNA and Rev1 via a PCNA-interacting protein (PIP) motif in its C-terminal unstructured region. PIP1 likely plays a critical role in the recruiting pol eta to the multi-protein complex. PIP2 likely plays a critical role in maintaining the architecture and the dynamics of this multi-protein complex needed to maximize the efficiency and accuracy of translesion synthesis
physiological function
Deinococcus radiodurans R1 / ATCC 13939 / DSM 20539
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involvement of deinococcal polymerase X in DNA-damage tolerance, possibly by contributing to DNA double-strand break repair and base excision repair
-
physiological function
-
the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis
-
physiological function
-
Dpo3 is a potential player in the proper maintenance of the archaeal genome
-
physiological function
-
the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis
-
physiological function
-
in translesion synthesis (TLS), specialized DNA polymerases, such as polymerase (pol) eta, are recruited to stalled replication forks. The polymerase form a multi-protein complex with PCNA, Rad6-Rad18, and other specialized polymerases. Pol eta interacts with PCNA and Rev1 via a PCNA-interacting protein (PIP) motif in its C-terminal unstructured region. PIP1 likely plays a critical role in the recruiting pol eta to the multi-protein complex. PIP2 likely plays a critical role in maintaining the architecture and the dynamics of this multi-protein complex needed to maximize the efficiency and accuracy of translesion synthesis
-
physiological function
-
in translesion synthesis (TLS), specialized DNA polymerases, such as polymerase (pol) eta, are recruited to stalled replication forks. The polymerase form a multi-protein complex with PCNA, Rad6-Rad18, and other specialized polymerases. Pol eta interacts with PCNA and Rev1 via a PCNA-interacting protein (PIP) motif in its C-terminal unstructured region. PIP1 likely plays a critical role in the recruiting pol eta to the multi-protein complex. PIP2 likely plays a critical role in maintaining the architecture and the dynamics of this multi-protein complex needed to maximize the efficiency and accuracy of translesion synthesis
-
additional information
-
binding and recognition of the correct dNTP, the recombinant enzyme performs several small steps like local conformational changes involving active site residues, reorganization of Mg2+-coordinating ligands, and proton transfer
additional information
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three aspartic acid residues D378, D380 and D531 form the catalytic carboxylate triad in pol E. Amino acid residues D378 and D531 are mainly responsible for the binding of metal chelated substrate dNTP, while D380 is solely responsible for the chemical step of phosphodiester bond formation
additional information
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the DNA polymerase V is comprised by the UmuD'2C protein complex. Pol V activity depends on the beta-clamp and gamma-clamp loaders UmuC and UmuD'2, overview
additional information
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the holoenzyme of pol gamma consists of a catalytic subunit and a dimeric form of its accessory subunit, interaction of the accessory subunit with the pol gamma catalytic subunit enhances the processivity bx 50fold and the DNA binding properties of the catalytic subunit. The catalytic subunit is a 140 kDa enzyme, i.e. p140, that contains an N-terminal exonuclease domain connected by a linker region to a C-terminal polymerase domain and has DNA polymerase, 3'->5' exonuclease and 5' dRP lyase activities. The accessory subunit is a 55 kDa protein, i.e. p55, required for tight DNA binding and processive DNA synthesis
additional information
-
the error frequency of the enzyme does not change significantly when the temperature is raised from 22°C to 72°C
additional information
structure modeling of K4 polymerase, overview
additional information
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nine residues, Tyr326, Leu329, Gln384, Lys387, Phe388, Met408, Asn422, Tyr438, and Phe451, are predicted to be involved in DNA/RNA distinction
additional information
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structural, kinetic and thermodynamic basis for the extraordinary accuracy of high-fidelity DNA polymerases, overview. The changes in enzyme structure following nucleotide binding govern the fate of the bound nucleotide, and the conformational change plays an essential role in establishing enzyme selectivity, conformational coupling between enzyme structure and fidelity, modeling of the universal mechanism: while the correct substrate induces a structure to facilitate catalysis, the wrong substrate induces a structure to slow catalysis and promote substrate release. Two-step sequence for nucleotide binding, two metal ion mechanism, nucleotide binds to the enzyme as an Mg-dNTP-2 complex, overview
additional information
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the incorporation of 8-oxo-dGTP and 3'-azido-3'-deoxythymidine 5'-triphosphate by the human mitochondrial DNA polymerase provides an exception to the general rule that diphosphate release is fast. Analysis of the burst kinetics during incorporation of 8-oxo-dGTP shows that the amplitude of the burst is dependent upon the nucleotide concentration, diphosphate release is extremely slow following the incorporation of 3'-azido-3'-deoxythymidine 5'-triphosphate. The reversible chemistry and slow release of diphosphate decreases the specificity constant for the incorporation of 3'-azido-3'-deoxythymidine 5'-triphosphate and 8-oxo-dGTP. Brownian ratchet model, overview
additional information
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replicative DNA polymerases use a complex, multistep mechanism for efficient and accurate DNA replication, kinetics and conformational dynamics by single-molecule Förster resonance energy transfer techniques, overview. The replicative polymerase can bind to DNA in at least three conformations, corresponding to an open and closed conformation of the finger domain as well as a conformation with the DNA substrate bound to the exonuclease active site of PolB1. PolB1 can transition between these conformations without dissociating from a primer-template DNA substrate. The closed conformation is promoted by a matched incoming dNTP but not by a mismatched dNTP and that mismatches at the primer-template terminus lead to an increase in the binding of the DNA to the exonuclease site
additional information
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the enzyme contains domains for binding ubiquitin and proliferating cell nuclear antigen
additional information
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physiological importance of the two different metal cofactors, the [4Fe-4S] cluster in CysB and Zn2+ in CysA, in the stabilization of DNA polymerase interactions with different accessory proteins essential for processive DNA synthesis at the replication fork. CysA is an important determinant for proliferating cell nuclear antigen binding
additional information
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physiological importance of the two different metal cofactors, the [4Fe-4S] cluster in CysB and Zn2+ in CysA, in the stabilization of DNA polymerase interactions with different accessory proteins essential for processive DNA synthesis at the replication fork. CysA is an important determinant for proliferating cell nuclear antigen binding
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additional information
-
nine residues, Tyr326, Leu329, Gln384, Lys387, Phe388, Met408, Asn422, Tyr438, and Phe451, are predicted to be involved in DNA/RNA distinction
-
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PDB
SCOP
CATH
UNIPROT
ORGANISM
Escherichia coli \'BL21-Gold(DE3)pLysS AG
Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
Streptococcus sp. \'group G