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Information on EC 2.7.7.7 - DNA-directed DNA polymerase and Organism(s) Saccharomyces cerevisiae and UniProt Accession P46957

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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.
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Saccharomyces cerevisiae
UNIPROT: P46957
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Word Map
The taxonomic range for the selected organisms is: Saccharomyces cerevisiae
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
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
DNA polymerase delta
-
Pol3
subunit of DNA polymerase delta
Pol31
subunit of DNA polymerase delta
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 2
-
-
DNA polymerase alpha
-
-
-
-
DNA polymerase epsilon
-
-
DNA polymerase eta
-
-
DNA polymerase gamma
-
-
-
-
DNA polymerase I
-
-
-
-
DNA polymerase II
-
-
-
-
DNA polymerase III
-
-
-
-
DNA polymerase IV
-
-
DNA replicase
-
-
-
-
DNA-dependent DNA polymerase
-
-
-
-
duplicase
-
-
-
-
Klenow fragment
-
-
-
-
mtDNA polymerase NI
-
nucleotidyltransferase, deoxyribonucleate
-
-
-
-
Pol gamma
-
-
-
-
polymerase alpha catalytic subunit A
-
RAD30
sequenase
-
-
-
-
Taq DNA polymerase
-
-
-
-
Taq Pol I
-
-
-
-
Tca DNA polymerase
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
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 hide
9012-90-2
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
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
-
-
?
dATP + DNAn
?
show the reaction diagram
-
-
-
-
?
dCTP + DNAn
?
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
rATP + DNAn
?
show the reaction diagram
-
-
-
-
?
rCTP + DNAn
?
show the reaction diagram
-
-
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
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
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
Mn2+
-
enzyme prefers Mn2+ over Mg2+ for RTHI nuclease activity
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
4-chloromercuribenzoic acid
-
-
aphidicolin
Dideoxythymidine triphosphate
-
-
Ethidium bromide
-
-
N-ethylmaleimide
-
-
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Polymerase alpha accessory factors
-
overview
-
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
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
1.22
purified DNA pol NI, pH 7.5, 37°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
-
polymerase alpha and gamma
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
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
physiological function
additional information
-
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
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
120000
-
mitochondrial enzyme
124000
-
polymerase delta, calculated from nucleotide sequence
125000
-
x * 125000 + x * 55000, polymerase delta
132000 - 200000
-
DNA polymerase epsilon
150000
-
polymerase I and II
170000
180000
-
x * 180000 + x * 86000 + x * 58000 + x * 48000, polymerase alpha
40000
-
1 * 40000, DNA polymerase beta
47000
-
SDS-PAGE
48000
-
x * 180000 + x * 86000 + x * 58000 + x * 48000, polymerase alpha
55000
-
x * 125000 + x * 55000, polymerase delta
58000
-
x * 180000 + x * 86000 + x * 58000 + x * 48000, polymerase alpha
60000
-
2 * 60000, SDS-PAGE, mitochondrial enzyme
86000
-
x * 180000 + x * 86000 + x * 58000 + x * 48000, polymerase alpha
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
trimer
Poldelta composed of the three subunits Pol3, Pol31, and Pol32, X-ray crystallography
dimer
monomer
-
1 * 40000, DNA polymerase beta
tetramer
-
isozymes pol alpha and epsilon contain subunits Pol1, Pol12, Pri1, and Pri2, Pol2, Dpb2, Dpb3 and Dpb4, respectively
trimer
-
isozyme pol delta contains subunits Pol3, Pol31 and Pol32
additional information
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
M644F
-
mutant enzyme has reduced fidelity resulting from strongly increased misinsertion rates
M644L
-
mutant enzyme synthesizes DNA with high fidelity
M644W
-
mutant enzyme synthesizes DNA with high fidelity
Y708A
-
mutation of pol delta, exhibits slow growth, sensitivity to hydroxyurea and strong mutator phenotype for frameshifts and base substitutions
Y831A
-
mutation of pol epsilon, slight sensitivity to hydroxyurea, semidominant mutator phenotype for frameshifts and base substitutions
Y869A
-
mutation of pol alpha, strain is viable, exhibits slow growth, sensitivity to hydroxyurea and spontaneous mutator phenotype for frameshifts and base substitutions
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
ammonium sulfate precipitation, glutathione-Sepharose column chromatography, Mono-Q column chromatography, and Superose 6 gel filtration
-
catalytic core of DNA polymerase eta (residues 1-513)
GST-tagged POL3, POL31, and POL32 by glutathione affinity chromatography
-
mitochondrial enzyme
-
native DNA pol NI or DNA polymerase alpha catalytic subunit A/DNA polymerase subunit alphabeta, POL12, 1700fold from mitochondria by cation and anion exchange chromatography, heparin affinity chromatography, and gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
catalytic core of DNA polymerase eta (residues 1-513)
gene POL1 encoding mitochondrial DNA pol NI or DNA polymerase alpha catalytic subunit A/DNA polymerase subunit alphabeta, POL12, DNA and amino acid sequence determination and analysis, expression as GFP-tagged enzyme in yeast strain BY4741
overview: genetic structure and predicted functional domains
-
polymerase delta, overproduced in Escherichia coli
-
recombinant expression of POL3 containing a cleavable N-terminal GST-tag, and of POL31 and POL32 from the galactose-inducible GAL1-10 promoter in protease-deficient strain BJ2168, expression of c-Myc-tagged catalytic subunits Pol1, Pol2, and Pol3 in Escherichia coli strain BL21. Expression of the C-terminal domain of Pol3 (amino acids 982-1097) with a N-terminal HA epitope tag or C-terminally Strep-tagged CTD domains of Pol1, Pol2, Pol3 in Escherichia coli strain HMS174 (DE3) pLysS
-
RENATURED/Commentary
ORGANISM
UNIPROT
LITERATURE
renatured by dialysis against decreasing concentrations of urea, optimal protein concentration for refolding: 0.005 mg/ml
-
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
Bambara, R.A.; Jessee, C.B.
Properties of DNA polymerases delta and epsilon, and their roles in eukaryotic DNA replication
Biochim. Biophys. Acta
1088
11-24
1991
Bos taurus, Saccharomyces cerevisiae, Oryctolagus cuniculus, Homo sapiens, Mammalia, Mus musculus
Manually annotated by BRENDA team
Brown, W.C.; Duncan, J.A.; Campbell, J.L.
Purification and characterization of the Saccharomyces cerevisiae DNA polymerase delta overproduced in Escherichia coli
J. Biol. Chem.
268
982-990
1993
Saccharomyces cerevisiae
Manually annotated by BRENDA team
Sen, S.; Mukhopadhyay, S.; Wetzel, J.; Biswas, T.K.
Characterization of the mitochondrial DNA polymerase from Saccharomyces cerevisiae
Acta Biochim. Pol.
41
79-86
1994
Saccharomyces cerevisiae
Manually annotated by BRENDA team
Wintersberger E.
DNA-dependent DNA pllymerases from eukaryotes
Trends Biochem. Sci.
1977
58-60
1977
Bos taurus, Saccharomyces cerevisiae, Homo sapiens, Rattus norvegicus
-
Manually annotated by BRENDA team
Scovassi, A.I.; Plevani, P.; Bertazzoni, U.
Eukaryotic DNA polymerases
Trends Biochem. Sci.
1980
335-337
1980
Bos taurus, Saccharomyces cerevisiae, Dictyostelium discoideum, Euglena gracilis, Homo sapiens, Mammalia, Neurospora crassa, Physarum polycephalum, Tetrahymena pyriformis, Trypanosoma brucei, Ustilago maydis
-
Manually annotated by BRENDA team
Pavlov, Y.I.; Shcherbakova, P.V.; Kunkel, T.A.
In vivo consequences of putative active site mutations in yeast DNA polymerases alpha, epsilon, delta, and zeta
Genetics
159
47-64
2001
Saccharomyces cerevisiae
Manually annotated by BRENDA team
Zhu, F.X.; Biswas, E.; Biswas, S.B.
Purification and characterization of the DNA polymerase alpha associated exonuclease: The RTH1 gene product
Biochemistry
36
5947-5954
1997
Saccharomyces cerevisiae
Manually annotated by BRENDA team
Bebenek, K.; Garcia-Diaz, M.; Patishall, S.R.; Kunkel, T.A.
Biochemical properties of Saccharomyces cerevisiae DNA polymerase IV
J. Biol. Chem.
280
20051-20058
2005
Saccharomyces cerevisiae
Manually annotated by BRENDA team
Tsubota, T.; Tajima, R.; Ode, K.; Kubota, H.; Fukuhara, N.; Kawabata, T.; Maki, S.; Maki, H.
Double-stranded DNA binding, an unusual property of DNA polymerase epsilon, promotes epigenetic silencing in Saccharomyces cerevisiae
J. Biol. Chem.
281
32898-32908
2006
Saccharomyces cerevisiae
Manually annotated by BRENDA team
Johnson, R.E.; Prakash, L.; Prakash, S.
Yeast and human translesion DNA synthesis polymerases: expression, purification, and biochemical characterization
Methods Enzymol.
408
390-407
2006
Saccharomyces cerevisiae, Homo sapiens
Manually annotated by BRENDA team
Pursell, Z.F.; Isoz, I.; Lundstroem, E.B.; Johansson, E.; Kunkel, T.A.
Regulation of B family DNA polymerase fidelity by a conserved active site residue: characterization of M644W, M644L and M644F mutants of yeast DNA polymerase epsilon
Nucleic Acids Res.
35
3076-3086
2007
Saccharomyces cerevisiae
Manually annotated by BRENDA team
Dhillon, N.; Raab, J.; Guzzo, J.; Szyjka, S.J.; Gangadharan, S.; Aparicio, O.M.; Andrews, B.; Kamakaka, R.T.
DNA polymerase epsilon, acetylases and remodellers cooperate to form a specialized chromatin structure at a tRNA insulator
EMBO J.
28
2583-2600
2009
Saccharomyces cerevisiae
Manually annotated by BRENDA team
Sabouri, N.; Johansson, E.
Translesion synthesis of abasic sites by yeast DNA polymerase epsilon
J. Biol. Chem.
284
31555-31563
2009
Saccharomyces cerevisiae
Manually annotated by BRENDA team
Jain, R.; Hammel, M.; Johnson, R.E.; Prakash, L.; Prakash, S.; Aggarwal, A.K.
Structural insights into yeast DNA polymerase delta by small angle X-ray scattering
J. Mol. Biol.
394
377-382
2009
Saccharomyces cerevisiae (P46957), Saccharomyces cerevisiae
Manually annotated by BRENDA team
Lasserre, J.P.; Plissonneau, J.; Velours, C.; Bonneu, M.; Litvak, S.; Laquel, P.; Castroviejo, M.
Biochemical, cellular and molecular identification of DNA polymerase alpha in yeast mitochondria
Biochimie
95
759-771
2013
Saccharomyces cerevisiae (P13382), Saccharomyces cerevisiae, Saccharomyces cerevisiae BY4742 (P13382)
Manually annotated by BRENDA team
Netz, D.J.; Stith, C.M.; Stuempfig, M.; Koepf, G.; Vogel, D.; Genau, H.M.; Stodola, J.L.; Lill, R.; Burgers, P.M.; Pierik, A.J.
Eukaryotic DNA polymerases require an iron-sulfur cluster for the formation of active complexes
Nat. Chem. Biol.
8
125-132
2012
Saccharomyces cerevisiae, Saccharomyces cerevisiae W303-1A
Manually annotated by BRENDA team
Xue, Q.; Zhong, M.; Liu, B.; Tang, Y.; Wei, Z.; Guengerich, F.; Zhang, H.
Kinetic analysis of bypass of 7,8-dihydro-8-oxo-2'-deoxyguanosine by the catalytic core of yeast DNA polymerase eta
Biochimie
121
161-169
2016
Saccharomyces cerevisiae (A6ZZ16), Saccharomyces cerevisiae YJM789 (A6ZZ16)
Manually annotated by BRENDA team
Ripley, B.M.; Reusch, D.T.; Washington, M.T.
Yeast DNA polymerase eta possesses two PIP-like motifs that bind PCNA and Rad6-Rad18 with different specificities
DNA Repair
95
102968
2020
Saccharomyces cerevisiae, [Candida] glabrata, Saccharomyces pastorianus, Torulaspora delbrueckii, Zygosaccharomyces rouxii, Saccharomyces paradoxus, Saccharomyces kudriavzevii, Vanderwaltozyma polyspora, Tetrapisispora phaffii, Naumovozyma dairenensis, Kazachstania naganishii, Kluyveromyces dobzhanskii, Lachancea fermentati, Lachancea lanzarotensis, Naumovozyma castellii, Tetrapisispora blattae, Saccharomyces arboricola (J8LJI8), Kluyveromyces marxianus (W0TAY7), Kluyveromyces marxianus DMKU3-1042 (W0TAY7), Saccharomyces arboricola H-6 (J8LJI8)
Manually annotated by BRENDA team