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2.7.7.7: DNA-directed DNA polymerase

This is an abbreviated version!
For detailed information about DNA-directed DNA polymerase, go to the full flat file.

Word Map on EC 2.7.7.7

Reaction

a 2'-deoxyribonucleoside 5'-triphosphate
+
DNAn
=
diphosphate
+
DNAn+1

Synonyms

3'–5'-exonuclease, ABO4/POL2a/TIL1, Afu polymerase, ASFV DNA polymerase, ASFV Pol X, B-family replicative DNA polymerase, beta type DNA polymerase, Bst DNA polymerase, CpDNApolI, DBH, Dbh DNA polymerase, Dbh polymerase, ddNTP-sensitive DNA polymerase, Deep Vent DNA polymerase, DeepVent DNA polymerase, deoxynucleate polymerase, deoxyribonucleate nucleotidyltransferase, deoxyribonucleic acid duplicase, deoxyribonucleic acid polymerase, deoxyribonucleic duplicase, deoxyribonucleic polymerase, deoxyribonucleic polymerase I, DinB DNA polymerase, DinB homologue, Dmpol zeta, DNA deoxynucleotidyltransferase, DNA duplicase, DNA nucleotidyltransferase, DNA nucleotidyltransferase (DNA-directed), DNA pol, DNA pol B1, DNA Pol eta, DNA Pol lambda, DNA pol NI, DNA pol Y1, DNA polmerase beta, DNA polymerase, DNA polymerase 1, DNA polymerase 2, DNA polymerase 4, DNA polymerase A, DNA polymerase alpha, DNA polymerase B, DNA polymerase B1, DNA polymerase B2, DNA polymerase B3, DNA polymerase beta, DNA polymerase D, DNA polymerase Dbh, 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 ny, DNA polymerase pyrococcus kodakaraensis, DNA polymerase theta, DNA polymerase V, DNA polymerase X, DNA polymerase zeta, DNA polymerases B, DNA polymerases D, DNA polymmerase I, DNA primase-polymerase, DNA replicase, DNA replication polymerase, DNA-dependent DNA polymerase, DNAP, DP1Pho, DP2Pho, Dpo1, Dpo2, Dpo3, Dpo4, Dpo4 polymerase, Dpo4-like enzyme, duplicase, error-prone DNA polymerase, error-prone DNA polymerase X, family B-type DNA polymerase, hoPolD, HSV 1 POL, Igni_0062, K4 polymerase, K4pol, K4PolI, kDNA replication protein, KDO XL DNA polymerase, KF(exo-), KF-, Klenow fragment, Klenow-like DNA polymerase I, KOD DNA polymerases, lesion-bypass DNA polymerase, M1 DNA polymerase, M1pol, MacDinB-1, MA_4027, Miranda pol beta protein, mitochondrial DNA polymerase, Mka polB, More, MsDpo4, mtDNA polymerase NI, mtDNA replicase, Neq DNA polymerase, non-replicative DNA polymerase III, nucleotidyltransferase, deoxyribonucleate, OsPOLP1, PabPol D, PabpolB, PabpolD, Pfu, Pfu DNA polymerase, Pfu Pol, Pfu-POl, PH0121, PH0123, phi29 DNA polymerase, phi29 DNApol, PhoPolD, phPol D, Pol, pol alpha, Pol B, Pol B1, pol beta, Pol BI, pol delta, pol E, POl epsilon, Pol eta, Pol gamma, Pol I, Pol II, pol III, pol iota, Pol IV, pol kappa, pol kappaDELTAC, Pol lambda, Pol mu, pol NI, Pol ny, Pol theta, Pol V, pol Vent (exo-), Pol X, Pol zeta, Pol-beta, POL1, Pol2, POL2a, Pol3, Pol31, PolB, POlB1, polbeta, polD, POLD4, Poldelta, POLdelta1, PolDPho, Polepsilon, Poleta, POLG, PolH, polI, POLIB, POLIC, POLID, poliota, Polkappa, PolX, PolY, poly iota, polymerase alpha catalytic subunit A, polymerase III, pORF30, Pwo DNA polymerase, R2 polymerase, R2 reverse transcriptase, R2-RT, RAD30, RB69 DdDp, RB69 DNA Polymerase, RB69pol, Rec1, repair polymerase, replicative DNA polymerase, reverse transcriptase, RKOD DNA polymerase, Rv1537, Rv3056, Saci_0554, sequenase, Sso, Sso DNA pol B1, Sso DNA pol Y1, Sso DNA polymerase Y1, Sso DNApol, Sso pol B1, SSO0552, SSO2448, SsoDpo1, SsoPolB1, SsoPolY, Szi DNA polymerase, T4 DNA polymerase, T7 DNA polymerase, Taq DNA polymerase, Taq Pol I, Taq polymerase, Tba5 DNA polymerase, Tca DNA polymerase, Tga PolB, TGAM_RS07365, Tkod-Pol, translesion DNA polymerase, translesion DNA synthesis polymerase, translesion polymerase Dpo4, UL30/UL42, UmuD'2C, UmuD'2C-RecA-ATP, Vent polymerase, X family DANN polymerase, Y-family DNA polymerase eta

ECTree

     2 Transferases
         2.7 Transferring phosphorus-containing groups
             2.7.7 Nucleotidyltransferases
                2.7.7.7 DNA-directed DNA polymerase

Inhibitors

Inhibitors on EC 2.7.7.7 - DNA-directed DNA polymerase

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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(2E)-2-(3-nitro-4-[[6-(trifluoromethyl)pyridin-3-yl]sulfanyl]benzylidene)-5-thioxo-1,3-thiazolidin-4-one
-
-
(2E)-2-(4-chloro-3-ethylbenzylidene)-5-thioxo-1,3-thiazolidin-4-one
-
-
(2E)-2-(pentafluorobenzylidene)-5-thioxodihydrothiophen-3(2H)-one
-
-
(2E)-2-[4-(2-hydroxyethyl)-3-nitrobenzylidene]-5-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-(4-chloro-3-nitrobenzylidene)-2-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-fluorobenzyl)oxy]benzylidene]-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
(E)-enedione
-
-
(NH4)2SO4
-
optimal concentration of 20 mM, inhibition below and above 20 mM
1,10-phenanthroline
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
1,3-bis[2-chloroethyl]-2-nitrosourea
-
-
1-deoxyrubralactone
10-epi pyragonicin
-
-
10-epi-pyragonicin
16-oxoaphidicholin
Tequatrovirus T4
-
-
19-epi jimenezin
-
-
19-epi-jimenezin
2',3'-dideoxy-ATP
-
poor inhibitor
2',3'-dideoxyribosylthymine triphosphate
2',3'-dideoxythymidine 5'-triphosphate
2-(4-azidophenacyl)thio-2'-deoxyadenosine 5'-triphosphate
-
template-competitive DNA polymerase inhibitor
-
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
2-butylanilino-dATP
-
potent and highly selective 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'-azido-2',3'-dideoxythymidine triphosphate
-
-
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
3,5-dimethyl-8-methoxy-3,4-dihydroisocoumarin
-
-
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
3-epiaphidicholine
Tequatrovirus T4
-
-
35dd(G) DNA
-
competitive inhibition
-
4-chloromercuribenzoic acid
4-chlorophenyl 2,4-dinitrophenyl sulfide
-
-
4-hydroxy-5-methyl-3-tetradecyl-dihydrofuran-2(3H)-one
-
-
4-hydroxymercuribenzoate
Tequatrovirus T4
-
95% inhibition at 0.4 mM
4-oxo-dihydroquinoline
-
binds at the polymerase active site interacting non-covalently with both the polymerase and the DNA duplex
4-[(4-methylphenyl)sulfanyl]-3-nitrobenzaldehyde
-
-
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
6-chloro-1,4-dihydro-4-oxo-1H-quinoline-3-carboxylic acid
-
-
acrolein
-
irreversible inhibition
acyclovir triphosphate
-
-
adefovir diphosphate
Allicin
alliin
alpha-(4-azidophenyl)-1,N6-etheno-dATP
-
template-competitive DNA polymerase inhibitor
alpha-Amanitin
Ruellia sp.
-
88% inhibition at 0.2 mg/ml
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
-
aphidicolin
aptamer
-
nucleotide ligands of small size and unique three-dimensional structure, TQ21 family, presence of loop is necessary for inhibition
-
ara-ATP
Ara-CTP
Arabinofuranosylnucleoside triphosphates
-
and related compounds
aurintricarboxylic acid
-
potent nanomolar inhibitor of pol beta, pol iota, and pol zeta
bakuchiol
Benzyloxycarbonyl-Leu-Leu-al
Ca2+
-
polymerase alpha
Carbonyldiphosphonate
catalpol
-
competitive
cerebroside sulfate ester
-
inhibition of polymerase alpha and gamma
cholesterol hemisuccinate
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
corylifolin
Betapolyomavirus macacae
-
isolated from Psoralea corylifolia
coumermycin A
-
50% inhibition at 0.05 mM
daidzein
Betapolyomavirus macacae
-
isolated from Psoralea corylifolia, slight inhibition
Dansyl-Leu-Leu-Leu-CH2Cl
dATP
-
using dATP as an inhibitor and dCTP as a varied substrate, the pattern of inhibition is competitive
ddTTP
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
diallyl pentasulfide
diallyl tetrasulfide
diallyl trisulfide
Dideoxyadenosine triphosphate
-
weak inhibitor
dideoxyguanosine triphosphate
-
-
Dideoxynucleoside 5'-triphosphate
Dideoxythymidine triphosphate
dimethyl sulfoxide
diphosphate
ellagic acid
-
potent nanomolar inhibitor of pol beta, pol iota, and pol zeta
epigallocatechin gallate
-
-
ethanol
Ethidium bromide
-
-
flavonoids
Ruellia sp.
-
substitution of hydroxyl groups with glycosides
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
glycerol
glycolipids
-
sulfate- and sialic acid-containing
-
Halenaquinol sulfate
hydroxyphenylazouracil
-
inhibits only polymerase III
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
iodoacetate
-
DNA polymerase beta
jimenezin
lamivudine triphosphate
Li+
-
polymerase alpha
lysophosphatidic acid
mucocin
muconin
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-ethylmaleimide
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-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
N2-CH2(6-benzo[a]pyrenyl)guanine
-
severely blocks activity
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
Betapolyomavirus macacae
-
isolated from Psoralea corylifolia, inhibition at moderate to high concentrations
NH4Cl
NSC-666715
potent, small molecular weight inhibitor of DNA polymerase beta, blocks Pol-beta-directed single-nucleotide- and long-patch-base excisison repair
Oosporein
pamoic acid
-
pol beta inhibitor
phosphate
Phosphoformate
Herpes simplex virus
-
-
Phosphonoacetate
plakevulin A
-
-
poly(rA)-p(dT)45
-
pyragonicin
pyranicin
pyridoxal 5'-phosphate
-
50% inhibition at 0.48 mM
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
-
resveratrol
Betapolyomavirus macacae
-
isolated from Psoralea corylifolia
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
-
SH-blocking agents
-
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
-
single-stranded DNA
Sodium dodecyl sulfate
-
-
sphingosine
-
polymerase alpha and beta
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
-
stavudine triphosphate
-
-
sucrose
-
50% inhibition with 4% sucrose
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
talaroflavone
tenofovir diphosphate
untenone A
-
-
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
zalcitabine triphosphate
-
-
zidovudine triphosphate
Zn2+
Herpes simplex virus
-
-
[3-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenoxy]acetic acid
-
-
additional information
-