DB code: M00173

RLCP classification 3.103.90020.1135 : Transfer
CATH domain 3.30.420.10 : Nucleotidyltransferase; domain 5
1.20.1060.10 : Taq DNA Polymerase; Chain T, domain 4
3.30.70.370 : Alpha-Beta Plaits Catalytic domain
1.10.150.20 : DNA polymerase; domain 1 Catalytic domain
E.C. 2.7.7.7
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
1.10.150.20 : DNA polymerase; domain 1 M00055 M00104 M00175 M00208 D00158
1.20.1060.10 : Taq DNA Polymerase; Chain T, domain 4 M00055 M00175
3.30.420.10 : Nucleotidyltransferase; domain 5 M00206 T00252 M00019 M00020 M00055 M00135 M00146 M00166 M00175 M00186
3.30.70.370 : Alpha-Beta Plaits M00055 M00104 M00175

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P00581 DNA polymerase
EC 2.7.7.7
T7 DNA polymerase
NP_041982.1 (Protein)
NC_001604.1 (DNA/RNA sequence)
PF00476 (DNA_pol_A)
[Graphical View]

KEGG enzyme name
DNA-directed DNA polymerase
DNA polymerase I
DNA polymerase II
DNA polymerase III
DNA polymerase alpha
DNA polymerase beta
DNA polymerase gamma
DNA nucleotidyltransferase (DNA-directed)
DNA nucleotidyltransferase (DNA-directed)
deoxyribonucleate nucleotidyltransferase
deoxynucleate polymerase
deoxyribonucleic acid duplicase
deoxyribonucleic acid polymerase
deoxyribonucleic duplicase
deoxyribonucleic polymerase
deoxyribonucleic polymerase I
DNA duplicase
DNA nucleotidyltransferase
DNA polymerase
DNA replicase
DNA-dependent DNA polymerase
duplicase
Klenow fragment
sequenase
Taq DNA polymerase
Taq Pol I
Tca DNA polymerase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P00581 DPOL_BPT7 Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Composed of two subunits. One is encoded by the phage and the other is encoded by the host thioredoxin.

KEGG Pathways
Map code Pathways E.C.
MAP00240 Pyrimidine metabolism
MAP00230 Purine metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00677 C00039 C00013 C00039
E.C.
Compound Magnesium Deoxynucleoside triphosphate DNA(n) Pyrophosphate DNA(n+1)
Type divalent metal (Ca2+, Mg2+) nucleotide nucleic acids phosphate group/phosphate ion nucleic acids
ChEBI 18420
29888
PubChem 888
1023
21961011
1t7pA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1skrA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1sksA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1skwA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1sl0A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1sl0C01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1sl1A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1sl2A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1t8eA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1tk0A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1tk5A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1tk8A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1tkdA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1x9mA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1x9sA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1x9wA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1t7pA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1skrA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1sksA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1skwA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1sl0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1sl0C02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1sl1A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1sl2A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1t8eA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1tk0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1tk5A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1tk8A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1tkdA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1x9mA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1x9sA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1x9wA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1t7pA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_MG Unbound Analogue:G-C-C-A-G-T-G-C-C-A-2DA (chain P) Unbound Unbound
1skrA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_MG Unbound Analogue:G-C-C-A-G-T-G-C-C-A-2DA (chain P) Unbound Unbound
1sksA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:G-G-C-C-A-G-T-G-C-C-2DT (chain P) Unbound Unbound
1skwA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:C-A-G-T-G-C-C-2DT (chain P) Unbound Unbound
1sl0A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:G-G-C-C-A-G-T-G-C-C-2DT (chain P) Unbound Unbound
1sl0C03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:G-G-C-C-A-G-T-G-C-C-2DT (chain Q) Unbound Unbound
1sl1A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:C-A-G-T-G-C-C-T-2DA (chain P) Unbound Unbound
1sl2A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_MG Unbound Analogue:C-A-G-T-G-C-C-T-2DA (chain P) Unbound Unbound
1t8eA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_MG Unbound Analogue:C-G-A-A-A-A-C-G-A-C-G-G-C-C-A-G-T-G-C-C-A-2DT (chain C) Unbound Unbound
1tk0A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_MG Unbound Analogue:C-G-G-C-C-A-G-T-G-C-C-A-DDG (chain P) Unbound Unbound
1tk5A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:G-C-C-A-G-T-G-C-C-A-DDG (chain P) Unbound Unbound
1tk8A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_MG Unbound Analogue:A-C-G-A-C-G-G-C-C-A-G-T-G-C-C-A-2DA (chain P) Unbound Unbound
1tkdA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_MG Unbound Analogue:C-G-A-C-G-G-C-C-A-G-T-G-C-C-A-DOC (chain C) Unbound Unbound
1x9mA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:G-T-A-G-T-G-T-G-A-2DT (chain C) Unbound Unbound
1x9sA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:G-G-T-A-G-T-G-T-G-A-2DT (chain P) Unbound Unbound
1x9wA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:G-G-T-A-G-T-G-T-G-A-2DT (chain C) Unbound Unbound
1t7pA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:DG3 Unbound Unbound Unbound
1skrA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:DAD Unbound Unbound Unbound
1sksA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1skwA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1sl0A04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:DAD Unbound Unbound Unbound
1sl0C04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:DAD Unbound Unbound Unbound
1sl1A04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1sl2A04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:DAD Unbound Unbound Unbound
1t8eA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:DCT Unbound Unbound Unbound
1tk0A04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:DCT Unbound Unbound Unbound
1tk5A04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1tk8A04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:D3T Unbound Unbound Unbound
1tkdA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:D3T Unbound Unbound Unbound
1x9mA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1x9sA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1x9wA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
PDB;1kfn, 1krp, 1ksp, 2kfn, 2kfz, 2kzm, 2kzz & literature [25]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1t7pA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1skrA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1sksA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1skwA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1sl0A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1sl0C01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1sl1A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1sl2A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1t8eA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1tk0A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1tk5A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1tk8A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1tkdA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1x9mA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1x9sA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1x9wA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1t7pA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1skrA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1sksA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1skwA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1sl0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1sl0C02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1sl1A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1sl2A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1t8eA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1tk0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1tk5A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1tk8A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1tkdA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1x9mA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1x9sA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1x9wA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1t7pA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
1skrA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
1sksA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
1skwA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
1sl0A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
1sl0C03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
1sl1A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
1sl2A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
1t8eA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
1tk0A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
1tk5A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
1tk8A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
1tkdA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
1x9mA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
1x9sA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
1x9wA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
1t7pA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 506;ARG 518;LYS 522;TYR 526 GLY 478
1skrA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 506;ARG 518;LYS 522;TYR 526 GLY 478
1sksA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 506;ARG 518;LYS 522;TYR 526 GLY 478
1skwA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 506;ARG 518;LYS 522;TYR 526 GLY 478
1sl0A04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 506;ARG 518;LYS 522;TYR 526 GLY 478
1sl0C04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 506;ARG 518;LYS 522;TYR 526 GLY 478
1sl1A04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 506;ARG 518;LYS 522;TYR 526 GLY 478
1sl2A04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 506;ARG 518;LYS 522;TYR 526 GLY 478
1t8eA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 506;ARG 518;LYS 522;TYR 526 GLY 478
1tk0A04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 506;ARG 518;LYS 522;TYR 526 GLY 478
1tk5A04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 506;ARG 518;LYS 522;TYR 526 GLY 478
1tk8A04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 506;ARG 518;LYS 522;TYR 526 GLY 478
1tkdA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 506;ARG 518;LYS 522;TYR 526 GLY 478
1x9mA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 506;ARG 518;LYS 522;TYR 526 GLY 478
1x9sA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 506;ARG 518;LYS 522;TYR 526 GLY 478
1x9wA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 506;ARG 518;LYS 522;TYR 526 GLY 478

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
p.254-256
[2]
Fig.4, p.61

References
[1]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS)
Medline ID 98101638
PubMed ID 9440688
Journal Nature
Year 1998
Volume 391
Pages 251-8
Authors Doublie S, Tabor S, Long AM, Richardson CC, Ellenberger T
Title Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution.
Related PDB 1t7p
Related UniProtKB P00581
[2]
Resource
Comments
Medline ID
PubMed ID 9519297
Journal Curr Opin Struct Biol
Year 1998
Volume 8
Pages 54-63
Authors Brautigam CA, Steitz TA
Title Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 15235589
Journal Nat Struct Mol Biol
Year 2004
Volume 11
Pages 784-90
Authors Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS, Ellenberger T
Title Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7.
Related PDB 1skr 1sks 1skw 1sl0 1sl1 1sl2
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 15297882
Journal EMBO J
Year 2004
Volume 23
Pages 3452-61
Authors Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel TA, Ellenberger T
Title Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase.
Related PDB 1t8e 1tk0 1tk5 1tk8 1tkd
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 15528277
Journal Proc Natl Acad Sci U S A
Year 2004
Volume 101
Pages 16186-91
Authors Dutta S, Li Y, Johnson D, Dzantiev L, Richardson CC, Romano LJ, Ellenberger T
Title Crystal structures of 2-acetylaminofluorene and 2-aminofluorene in complex with T7 DNA polymerase reveal mechanisms of mutagenesis.
Related PDB 1x9m 1x9s 1x9w
Related UniProtKB

Comments
Although this enzyme belongs to the DNA polymerase type-A family, giving different global structure from that of the type-B family, the active site is very similar to that of type-B family. Thus, the catalytic mechanism must be similar to that of type-B family (M00019, M00020 in EzCatDB).
According to the literature [1] & [2], the catalytic reaction of polymerase domains proceeds as follows:
(1) The metal ion A (bound to Asp475 & Asp654) activates 3'-OH of DNA by lowering its pKa.
(2) The activated 3'-O atom makes a nucleophilic attack on the alpha-phosphate group of dNTP, forming a pentacoordinated transition-state.
(3) The negative charges on the transferred group (alpha-phoshate) and the leaving group (beta-phosphate and gamma-phosphate) are stabilized by the metal ions and stabilizers on the fourth domain (Gly478, His506, Arg518, Lys522, & Tyr526). According to the literature [1], Lys522 stabilizes the transferred alpha-phosphate, which is also stabilzed by both A and B metal ions. His506 and Tyr526 stabilize beta-phosphate, along with the metal ion B, Arg518 stabilizes gamma-phosphate together with the metal ion B (see [1]).
This enzyme belongs to the DNA polymerase type-A family.

Created Updated
2004-03-03 2009-02-26