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Information on EC 2.7.7.7 - DNA-directed DNA polymerase and Organism(s) Rattus norvegicus
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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: Rattus norvegicus
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
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn = diphosphate + DNAn+1
mechanism
-
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
additional information
?
-
-
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
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
polymerase alpha: role in DNA replication
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
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
-
-
?
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
-
polymerase alpha: role in DNA replication
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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
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
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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
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
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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
0.0096
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
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
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
643594, 643611, 643613, 643624, 643628, 643649, 671793, 672254, 691213, 691631, 692423, 692685, 702387, 721656
-
-
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
-
-
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
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_RAT
1451
0
165306
Swiss-Prot
other Location (Reliability: 1)
DPOG1_RAT
1216
0
136856
Swiss-Prot
Mitochondrion (Reliability: 3)
DPOLB_RAT
335
0
38327
Swiss-Prot
other Location (Reliability: 2)
DPOLL_RAT
573
0
62401
Swiss-Prot
other Location (Reliability: 2)
DPOD1_RAT
1103
0
123601
Swiss-Prot
other Location (Reliability: 2)
D4A628_RAT
2547
0
281653
TrEMBL
Mitochondrion (Reliability: 4)
F7F6Z7_RAT
515
0
58138
TrEMBL
Mitochondrion (Reliability: 2)
A0A158UYG2_RAT
727
0
81316
TrEMBL
other Location (Reliability: 1)
A0A8I6ASB4_RAT
566
0
61643
TrEMBL
other Location (Reliability: 2)
G3V8M1_RAT
1103
0
123574
TrEMBL
other Location (Reliability: 2)
Q66HH0_RAT
495
0
56178
TrEMBL
Mitochondrion (Reliability: 1)
D3Z8X4_RAT
2283
0
262143
TrEMBL
Mitochondrion (Reliability: 5)
A0A8I6A9L7_RAT
547
0
62144
TrEMBL
other Location (Reliability: 1)
F1M8G6_RAT
3132
0
351898
TrEMBL
other Location (Reliability: 2)
A0A8I6G330_RAT
316
0
36391
TrEMBL
other Location (Reliability: 2)
F1LRJ6_RAT
1429
0
162729
TrEMBL
other Location (Reliability: 1)
Q64619_RAT
20
0
2190
TrEMBL
other Location (Reliability: 1)
A0A096MK13_RAT
1468
0
167264
TrEMBL
other Location (Reliability: 1)
Q5RJZ4_RAT
314
0
36302
TrEMBL
other Location (Reliability: 2)
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
40000
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure of catalytic domain of rat DNA polymerase beta, hanging drop vapor diffusion method
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
R258A |
-
mutant of Pol beta has a facilitated subdomain-reopening step. Rate of single-nucleotide incorporation catalyzed by R258A is identical to that of wild-type
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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
Weissbach, A.
Cellular and viral-induced eukaryotic polymerases
The Enzymes,3rd Ed. (Boyer,P. D. ,ed. )
14
67-86
1981
Bos taurus, Gallus gallus, Herpes simplex virus, Homo sapiens, Mammalia, Mus musculus, Rattus norvegicus, Vaccinia virus
-
Davies II, J.F.; Almassy, R.J.; Hostomska, Z.; Ferre, R.A.; Hostomsky, Z.
2.3 A crystal structure of the catalytic domain of DNA polymerase beta
Cell
76
1123-1133
1994
Rattus norvegicus
Shirakihara, Y.; Matsukage, A.; Nishimoto, Y.; Date, T.
Crystallization of 31 kDa C-terminal fragment of rat DNA polymerase beta
J. Mol. Biol.
235
1342-1344
1994
Rattus norvegicus
Taguchi, T.; Matsukage, A.; Ito, H.; Saito, Y.; Kawashima, S.
Inhibition of DNA polymerases by tripeptide derivative protease inhibitors
Biochem. Biophys. Res. Commun.
185
1133-1140
1992
Escherichia coli, Rattus norvegicus
Sawaya, M.R.; Pelletier, H.; Kumar, A.; Wilson, S.H.; Kraut, J.
Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism
Science
264
1930-1935
1994
Rattus norvegicus
Wintersberger E.
DNA-dependent DNA pllymerases from eukaryotes
Trends Biochem. Sci.
1977
58-60
1977
Bos taurus, Saccharomyces cerevisiae, Homo sapiens, Rattus norvegicus
-
Ishimaru, C.; Kuriyama, I.; Shimazaki, N.; Koiwai, O.; Sakaguchi, K.; Kato, I.; Yoshida, H.; Mizushina, Y.
Cholesterol hemisuccinate: a selective inhibitor of family X DNA polymerases
Biochem. Biophys. Res. Commun.
354
619-625
2007
Bos taurus, Homo sapiens, Rattus norvegicus
Bakhtina, M.; Roettger, M.P.; Kumar, S.; Tsai, M.D.
A unified kinetic mechanism applicable to multiple DNA polymerases
Biochemistry
46
5463-5472
2007
African swine fever virus, Escherichia coli, Rattus norvegicus
Naganuma, M.; Nishida, M.; Kuramochi, K.; Sugawara, F.; Yoshida, H.; Mizushina, Y.
1-deoxyrubralactone, a novel specific inhibitor of families X and Y of eukaryotic DNA polymerases from a fungal strain derived from sea algae
Bioorg. Med. Chem.
16
2939-2944
2008
Tequatrovirus T4, Bos taurus, Brassica oleracea, Escherichia coli, Homo sapiens, Rattus norvegicus, Thermus aquaticus
Sasaki, R.; Suzuki, Y.; Yonezawa, Y.; Ota, Y.; Okamoto, Y.; Demizu, Y.; Huang, P.; Yoshida, H.; Sugimura, K.; Mizushina, Y.
DNA polymerase gamma inhibition by vitamin K3 induces mitochondria-mediated cytotoxicity in human cancer cells
Cancer Sci.
99
1040-1048
2008
Bos taurus, Homo sapiens, Rattus norvegicus
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
Makarova, A.V.; Tarantul, V.Z.; Gening, L.V.
Evolution of DNA polymerase iota structure and function in eukaryotes
Biochemistry
73
346-352
2008
Canis lupus familiaris, Gallus gallus, Coturnix coturnix, Oryctolagus cuniculus, Misgurnus fossilis, Mus musculus, Rana temporaria, Rattus norvegicus, Triturus cristatus, Testudines agrionemys, Philothamnus punctatus
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