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Information on EC 2.7.7.7 - DNA-directed DNA polymerase and Organism(s) Drosophila melanogaster
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2.7.7.7 DNA-directed DNA polymeraseIUBMB 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.
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Word Map
- 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
The taxonomic range for the selected organisms is: Drosophila melanogaster
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
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
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
deoxynucleate polymerase
-
-
-
-
deoxyribonucleate nucleotidyltransferase
-
-
-
-
deoxyribonucleic acid duplicase
-
-
-
-
deoxyribonucleic acid polymerase
-
-
-
-
deoxyribonucleic duplicase
-
-
-
-
deoxyribonucleic polymerase
-
-
-
-
deoxyribonucleic polymerase I
-
-
-
-
DNA duplicase
-
-
-
-
DNA nucleotidyltransferase
-
-
-
-
DNA nucleotidyltransferase (DNA-directed)
-
-
-
-
DNA polmerase beta
-
-
-
-
DNA polymerase
DNA polymerase alpha
-
-
-
-
DNA polymerase gamma
DNA polymerase I
-
-
-
-
DNA polymerase II
-
-
-
-
DNA polymerase III
-
-
-
-
DNA replicase
-
-
-
-
DNA-dependent DNA polymerase
-
-
-
-
duplicase
-
-
-
-
Klenow fragment
-
-
-
-
nucleotidyltransferase, deoxyribonucleate
-
-
-
-
Pol gamma
sequenase
-
-
-
-
Taq DNA polymerase
-
-
-
-
Taq Pol I
-
-
-
-
Tca DNA polymerase
-
-
-
-
DNA polymerase
-
-
-
-
DNA polymerase gamma
-
-
-
-
Pol gamma
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
mechanism
-
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
overview: basic mechanism of replicative DNA polymerases alpha and delta
-
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
mechanism of polymerase translocation along templates
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
nucleotidyl group transfer
-
-
-
-
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.
CAS REGISTRY NUMBER
COMMENTARY
9012-90-2
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA substrate: gapped duplex or single-stranded 5'-ends smaller than 100 nucleotides, pol I, pol II and pol III
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 3'--5' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
interaction of polymerases with template-primers containing chemically modified or damaged bases
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
fidelity of DNA replication
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase delta: with its auxiliary factor i.e. proliferating cell nuclear antigen, largely responsible for leading-strand synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
overview: physiological roles in replication and in DNA repair synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase gamma: required for mitochondrial DNA replication but encoded in the nucleus
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase alpha: with its associated primase largely responsible for lagging-strand synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
preference for poly(dA)/oligo(dT)10:1 as a template primer and has high processivity for DNA synthesis
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase delta: with its auxiliary factor i.e. proliferating cell nuclear antigen, largely responsible for leading-strand synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
overview: physiological roles in replication and in DNA repair synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase gamma: required for mitochondrial DNA replication but encoded in the nucleus
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase alpha: with its associated primase largely responsible for lagging-strand synthesis
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
DNA polymerase alpha
Carbonyldiphosphonate
-
DNA polymerase delta; no inhibition of polymerase alpha
Mg2+
-
DNA polymerase alpha: free Mg2+ competes with primer for enzyme binding, dramatic inhibition at Mg2+ concentration above the optimum
Mn2+
-
inhibits 3'-5'-proofreading activity, thereby decreasing the fidelity of DNA replication by 50%
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
inhibition at 0.1 mM
single-stranded DNA
-
inhibition of polymerase alpha, competitive with respect to activated DNA substrate
aphidicolin
-
DNA polymerase alpha; DNA polymerase delta; DNA polymerase epsilon
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
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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
-
proliferating cell nuclear antigen
-
PCNA, specific auxiliary factor stimulating DNA polymerase delta
-
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
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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
0.0089
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
0.014
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
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
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
-
-
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). DPOLA_DROME
1488
0
169903
Swiss-Prot
other Location (Reliability: 2)
POLI_DROME
737
0
80390
Swiss-Prot
other Location (Reliability: 2)
DPOG1_DROME
1145
0
129828
Swiss-Prot
Mitochondrion (Reliability: 3)
DPOZ_DROME
2130
0
240073
Swiss-Prot
other Location (Reliability: 2)
DPOLQ_DROME
2059
0
229873
Swiss-Prot
other Location (Reliability: 2)
DPOD1_DROME
1092
0
124905
Swiss-Prot
other Location (Reliability: 2)
POLH_DROME
885
0
99026
Swiss-Prot
other Location (Reliability: 4)
DPOE1_DROME
2236
0
256702
Swiss-Prot
other Location (Reliability: 2)
C6TP90_DROME
909
0
104625
TrEMBL
Secretory Pathway (Reliability: 1)
Q9GV40_DROME
2220
0
255022
TrEMBL
other Location (Reliability: 2)
G3M399_DROME
2236
0
256638
TrEMBL
other Location (Reliability: 2)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
182000
-
x * 182000 (alpha) + x * 60000 (beta) + x * 50000 (gamma), core polymerase
50000
-
x * 182000 (alpha) + x * 60000 (beta) + x * 50000 (gamma), core polymerase
60000
-
x * 182000 (alpha) + x * 60000 (beta) + x * 50000 (gamma), core polymerase
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
additional information
?
-
x * 182000 (alpha) + x * 60000 (beta) + x * 50000 (gamma), core polymerase
additional information
-
multipolypeptide complex in prokaryotes and eukaryotes, three structural levels can be distinguished: 1. core polymerase (responsible for basic polymerization step), 2. DNA polymerase holoenzyme (composed of the core polymerase, which is responsible for the basic polymerization step and associated accessory proteins, a complex which is fully active on naturally occuring DNA templates), 3. holoenzyme embedded in a higher order structure, such as an asymmetric dimer or other complex which acts in concert with other known replication enzymes
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
DELTA413470
-
mutation in the spacer region of the alpha-subunit. Obtained in small amounts due to low solubility, mutant has barely detectable DNA polymerase activity
DELTA483533
-
expressed efficiently and purified as soluble holoenzyme complex associated with wild-type beta-subunit. The DNA polymerase activity of the mutant holoenzyme is reduced greatly as compared to wild type
DELTA536581
-
expressed efficiently and purified as soluble holoenzyme complex associated with wild-type beta-subunit. The DNA polymerase activity of the mutant enzyme is 80% of wild-type holoenzyme
DELTA666742
-
mutation in the spacer region of the alpha-subunit. Obtained in small amounts due to low solubility, mutant has barely detectable DNA polymerase activity
F576A
-
mutation in alpha-subunit, mutant enzyme retains about 50% of wild-type activity
G575A
-
mutation in alpha-subunit, mutant enzyme has nearly normal activity
G575A/W576A/F578A
-
mutation in alpha-subunit completely reduces DNA polymerase activity
K557A
-
mutation in alpha-subunit, mutant enzyme has nearly normal activity
K687A/D688A/F689A
-
mutation in alpha-subunit resulted in DNA polymerase activities that is 6080% of wild-type enzyme
L558A
-
mutation in alpha-subunit, mutant enzyme retains about 50% of wild-type activity
P556A
-
mutation in alpha-subunit, mutant enzyme has nearly normal activity
P556A/K557A/L558A
-
mutation in alpha-subunit completely reduces DNA polymerase activity
S719A/Y720A/W721
-
mutation in alpha-subunit completely reduces DNA polymerase activity
Y419A/E420A/D421A
-
mutation in alpha-subunit resulted in DNA polymerase activities that is 6080% of wild-type enzyme
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
mutant proteins expressed from baculovirus constructs in insect cells
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Fisher, P.A.
Enzymologic mechanism of replicative DNA polymerases in higher eukaryotes
Prog. Nucleic Acid Res. Mol. Biol.
47
371-397
1994
Drosophila melanogaster, Homo sapiens
Wang, T.S.F.
Eukaryotic DNA polymerases
Annu. Rev. Biochem.
60
513-552
1991
Bos taurus, Saccharomyces cerevisiae, Gallus gallus, Drosophila melanogaster, Homo sapiens, Mammalia, Rattus norvegicus, Xenopus laevis
Lehman, I.R.; Karguni, L.S.
DNA polymerase alpha
J. Biol. Chem.
264
4265-4268
1989
Chlorocebus aethiops, Bos taurus, Saccharomyces cerevisiae, Drosophila melanogaster, Homo sapiens, Mammalia, Mus musculus
Hbscher, U.
DNA polymerase holoenzymes
Trends Biochem. Sci.
9
390-393
1984
Bos taurus, Drosophila melanogaster, Escherichia coli
-
Aoyagi, N.; Matsuoka, S.; Furunobu, A; Matsukage, A.; Sakaguchi, K.
Drosophila DNA polymerase delta. Purification and characterization
J. Biol. Chem.
169
6045-5050
1994
Drosophila melanogaster
-
Peck, V.M.; Germer, E.W.; Cress, A.E.
delta-type DNA polymerase characterized from Drosophila melanogaster embryos
Nucleic Acids Res.
20
5779-5784
1992
Drosophila melanogaster
Takeuchi, R.; Oshige, M.; Uchida, M.; Ishikawa, G.; Takata, K.; Shimanouchi, K.; Kanai, Y.; Ruike, T.; Morioka, H.; Sakaguchi, K.
Purification of Drosophila DNA polymerase zeta by REV1 protein-affinity chromatography
Biochem. J.
382
535-543
2004
Drosophila melanogaster
Luo, N.; Kaguni, L.S.
Mutations in the spacer region of Drosophila mitochondrial DNA polymerase affect DNA binding, processivity, and the balance between Pol and Exo function
J. Biol. Chem.
280
2491-2497
2005
Drosophila melanogaster
Oshige, M.; Takeuchi, R.; Ruike, R.; Kuroda, K.; Sakaguchi, K.
Subunit protein-affinity isolation of Drosophila DNA polymerase epsilon catalytic subunit
Protein Expr. Purif.
35
248-256
2004
Drosophila melanogaster
Mazzucco, C.E.; Hamatake, R.K.; Colonno, R.J.; Tenney, D.J.
Entecavir for treatment of hepatitis B virus displays no in vitro mitochondrial toxicity or DNA polymerase gamma inhibition
Antimicrob. Agents Chemother.
52
598-605
2008
Drosophila melanogaster
Nishida, M.; Hada, T.; Kuramochi, K.; Yoshida, H.; Yonezawa, Y.; Kuriyama, I.; Sugawara, F.; Yoshida, H.; Mizushina, Y.
Diallyl sulfides: Selective inhibitors of family X DNA polymerases from garlic (Allium sativum L.)
Food Chem.
108
551-560
2008
Tequatrovirus T4, Bos taurus, Brassica oleracea, Drosophila melanogaster, Escherichia coli, Homo sapiens, Rattus norvegicus, Thermus aquaticus, Oncorhynchus masou
Takahashi, S.; Yonezawa, Y.; Kubota, A.; Ogawa, N.; Maeda, K.; Koshino, H.; Nakata, T.; Yoshida, H.; Mizushina, Y.
Pyranicin, a non-classical annonaceous acetogenin, is a potent inhibitor of DNA polymerase, topoisomerase and human cancer cell growth
Int. J. Oncol.
32
451-458
2008
Tequatrovirus T4, Bos taurus, Brassica oleracea, Drosophila melanogaster, Escherichia coli, Homo sapiens, Rattus norvegicus, Thermus aquaticus, Oncorhynchus masou
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