DB code: M00020

RLCP classification 3.103.90020.1134 : Transfer
CATH domain 3.30.342.10 : DNA Polymerase; Chain A, domain 1
3.30.420.10 : Nucleotidyltransferase; domain 5
3.90.-.- : Catalytic domain
1.-.-.- : Catalytic domain
1.20.-.- :
3.-.-.- :
E.C. 2.7.7.7
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.30.420.10 : Nucleotidyltransferase; domain 5 M00206 T00252 M00019 M00055 M00135 M00146 M00166 M00173 M00175 M00186

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
Q38087 DNA polymerase
EC 2.7.7.7
Gp43
NP_861746.1 (Protein)
NC_004928.1 (DNA/RNA sequence)
PF00136 (DNA_pol_B)
PF03104 (DNA_pol_B_exo1)
[Graphical View]
P04415 DNA polymerase
EC 2.7.7.7
Gp43
NP_049662.1 (Protein)
NC_000866.4 (DNA/RNA sequence)
PF00136 (DNA_pol_B)
PF03104 (DNA_pol_B_exo1)
[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
P04415 DPOL_BPT4 Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
Q38087 DPOL_BPR69 Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).

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

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C02148 C00677 C00039 C00013 C00039
E.C.
Compound Divalent metal Deoxynucleoside triphosphate DNA(n) Pyrophosphate DNA(n+1)
Type divalent metal (Ca2+, Mg2+) nucleotide nucleic acids phosphate group/phosphate ion nucleic acids
ChEBI 29888
PubChem 1023
21961011
1clqA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ig9A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ih7A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9xA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9xB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9xC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9xD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9yA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1rv2A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1rv2B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1rv2C01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1rv2D01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1wafA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1wafB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1wajA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1noyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1noyB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1nozA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1nozB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1clqA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ig9A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ih7A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9xA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9xB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9xC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9xD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9yA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1rv2A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1rv2B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1rv2C02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1rv2D02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1wafA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1wafB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1wajA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1noyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1noyB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1nozA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1nozB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1clqA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:_CA Unbound Unbound Unbound Unbound
1ig9A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:2x_CA Bound:TTP Analogue:G-C-G-G-A-C-T-G-C-T-T-A-C-DOC (chain P) Unbound Unbound
1ih7A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9xA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:2x_CA Unbound Analogue:G-C-G-G-A-C-T-G-C-T-T-A-C-DOC (chain I) Unbound Unbound
1q9xB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:2x_CA Analogue:DGP_908 Analogue:G-C-G-G-A-C-T-G-C-T-T-A-C-DOC (chain J) Unbound Unbound
1q9xC03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:2x_CA Analogue:DGP_908 Analogue:G-C-G-G-A-C-T-G-C-T-T-A-C-DOC (chain K) Unbound Unbound
1q9xD03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:2x_CA Analogue:DGP_908 Analogue:G-C-G-G-A-C-T-G-C-T-T-A-C-DOC (chain L) Unbound Unbound
1q9yA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:2x_CA Bound:DCP Analogue:G-C-G-G-A-C-T-G-C-T-T-A-C-DOC (chain P) Unbound Unbound
1rv2A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:G-C-G-G-C-T-G-T-C-A-T-A-A-G-A (chain F)
1rv2B03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1rv2C03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:G-C-G-G-C-T-G-T-C-A-T-A-A-G-A (chain J)
1rv2D03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1wafA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1wafB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1wajA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1clqA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ig9A04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ih7A04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9xA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9xB04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9xC04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9xD04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9yA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1rv2A04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1rv2B04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1rv2C04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1rv2D04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1wafA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1wafB04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1wajA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1clqA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ig9A05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ih7A05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9xA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9xB05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9xC05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9xD05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9yA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1rv2A05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1rv2B05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1rv2C05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1rv2D05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1wafA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1wafB05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1wajA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1clqA06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ig9A06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ih7A06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9xA06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9xB06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9xC06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9xD06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1q9yA06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1rv2A06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1rv2B06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1rv2C06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1rv2D06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1wafA06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1wafB06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1wajA06 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.
literature [9]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1clqA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ig9A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ih7A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1q9xA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1q9xB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1q9xC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1q9xD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1q9yA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1rv2A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1rv2B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1rv2C01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1rv2D01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1wafA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1wafB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1wajA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1noyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1noyB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1nozA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1nozB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1clqA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ig9A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ih7A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1q9xA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1q9xB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1q9xC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1q9xD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1q9yA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1rv2A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1rv2B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1rv2C02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1rv2D02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1wafA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1wafB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1wajA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1noyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1noyB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1nozA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1nozB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1clqA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 411;LEU 412;ASP 623;SER 624(metal binding)
1ig9A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 411;LEU 412;ASP 623;SER 624(metal binding)
1ih7A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 411;LEU 412;ASP 623;SER 624(metal binding)
1q9xA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 411;LEU 412;ASP 623;SER 624(metal binding)
1q9xB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 411;LEU 412;ASP 623;SER 624(metal binding)
1q9xC03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 411;LEU 412;ASP 623;SER 624(metal binding)
1q9xD03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 411;LEU 412;ASP 623;SER 624(metal binding)
1q9yA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 414;LEU 415;ASP 626;SER 627(metal binding)
1rv2A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 411;LEU 412;ASP 623;SER 624(metal binding)
1rv2B03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 411;LEU 412;ASP 623;SER 624(metal binding)
1rv2C03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 411;LEU 412;ASP 623;SER 624(metal binding)
1rv2D03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 411;LEU 412;ASP 623;SER 624(metal binding)
1wafA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 411;LEU 412;ASP 623;SER 624(metal binding)
1wafB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 411;LEU 412;ASP 623;SER 624(metal binding)
1wajA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 411;LEU 412;ASP 623;SER 624(metal binding)
1clqA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 482;LYS 486;LYS 560;ASN 564
1ig9A04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 482;LYS 486;LYS 560;ASN 564
1ih7A04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 482;LYS 486;LYS 560;ASN 564
1q9xA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 482;LYS 486;LYS 560;ASN 564
1q9xB04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 482;LYS 486;LYS 560;ASN 564
1q9xC04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 482;LYS 486;LYS 560;ASN 564
1q9xD04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 482;LYS 486;LYS 560;ASN 564
1q9yA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 485;LYS 489;LYS 563;ASN 567
1rv2A04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 482;LYS 486;LYS 560;ASN 564
1rv2B04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 482;LYS 486;LYS 560;ASN 564
1rv2C04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 482;LYS 486;LYS 560;ASN 564
1rv2D04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 482;LYS 486;LYS 560;ASN 564
1wafA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 482;LYS 486;LYS 560;ASN 564
1wafB04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 482;LYS 486;LYS 560;ASN 564
1wajA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 482;LYS 486;LYS 560;ASN 564
1clqA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ig9A05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ih7A05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1q9xA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1q9xB05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1q9xC05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1q9xD05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1q9yA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1rv2A05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1rv2B05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1rv2C05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1rv2D05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1wafA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1wafB05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1wajA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1clqA06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ig9A06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ih7A06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1q9xA06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1q9xB06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1q9xC06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1q9xD06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1q9yA06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1rv2A06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1rv2B06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1rv2C06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1rv2D06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1wafA06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1wafB06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1wajA06 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
Fig.3, p.192 2
[9]
Fig.4, p.61
[11]
p.8100
[20]
p.661-665

References
[1]
Resource
Comments
Medline ID
PubMed ID 1349852
Journal Cell
Year 1992
Volume 69
Pages 425-37
Authors Kong XP, Onrust R, O'Donnell M, Kuriyan J
Title Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 1314195
Journal FEBS Lett
Year 1992
Volume 300
Pages 141-4
Authors Strick R, Knopf CW
Title Improved band shift assay for the simultaneous analysis of protein-DNA interactions and enzymatic functions of DNA polymerases.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 7903401
Journal J Mol Biol
Year 1993
Volume 234
Pages 915-25
Authors Kuriyan J, O'Donnell M
Title Sliding clamps of DNA polymerases.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 8594347
Journal Methods Enzymol
Year 1995
Volume 262
Pages 189-202
Authors Eckstein F, Thomson JB
Title Phosphate analogs for study of DNA polymerases.
Related PDB
Related UniProtKB
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 1-388.
Medline ID 96292335
PubMed ID 8679562
Journal Biochemistry
Year 1996
Volume 35
Pages 8110-9
Authors Wang J, Yu P, Lin TC, Konigsberg WH, Steitz TA
Title Crystal structures of an NH2-terminal fragment of T4 DNA polymerase and its complexes with single-stranded DNA and with divalent metal ions.
Related PDB 1noy 1noz
Related UniProtKB P04415
[6]
Resource
Comments
Medline ID
PubMed ID 9265627
Journal Biochemistry
Year 1997
Volume 36
Pages 10474-81
Authors Goodrich LD, Lin TC, Spicer EK, Jones C, Konigsberg WH
Title Residues at the carboxy terminus of T4 DNA polymerase are important determinants for interaction with the polymerase accessory proteins.
Related PDB
Related UniProtKB
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
Medline ID 97358535
PubMed ID 9215631
Journal Cell
Year 1997
Volume 89
Pages 1087-99
Authors Wang J, Sattar AK, Wang CC, Karam JD, Konigsberg WH, Steitz TA
Title Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69.
Related PDB 1waf 1waj
Related UniProtKB Q38087
[8]
Resource
Comments
Medline ID
PubMed ID 9665721
Journal Biochemistry
Year 1998
Volume 37
Pages 10156-63
Authors Otto MR, Bloom LB, Goodman MF, Beechem JM
Title Stopped-flow fluorescence study of precatalytic primer strand base-unstacking transitions in the exonuclease cleft of bacteriophage T4 DNA polymerase.
Related PDB
Related UniProtKB
[9]
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
[10]
Resource
Comments
Medline ID
PubMed ID 10387009
Journal Biochemistry
Year 1999
Volume 38
Pages 7696-709
Authors Alley SC, Shier VK, Abel-Santos E, Sexton DJ, Soumillion P, Benkovic SJ
Title Sliding clamp of the bacteriophage T4 polymerase has open and closed subunit interfaces in solution.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 10387055
Journal Biochemistry
Year 1999
Volume 38
Pages 8094-101
Authors Yang G, Lin T, Karam J, Konigsberg WH
Title Steady-state kinetic characterization of RB69 DNA polymerase mutants that affect dNTP incorporation.
Related PDB
Related UniProtKB
[12]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF COMPLEX WITH GP45.
Medline ID 20004392
PubMed ID 10535734
Journal Cell
Year 1999
Volume 99
Pages 155-66
Authors Shamoo Y, Steitz TA
Title Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex.
Related PDB 1clq 1b8h
Related UniProtKB Q38087
[13]
Resource
Comments
Medline ID
PubMed ID 10616725
Journal Nucleosides Nucleotides
Year 1999
Volume 18
Pages 2193-9
Authors Stattel JM, Wright GE
Title Sensitivity of bacteriophage RB69 DNA polymerase to N2-(p-n-butylphenyl)-2'-deoxyguanosine nucleotides.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 10097083
Journal Proc Natl Acad Sci U S A
Year 1999
Volume 96
Pages 3600-5
Authors Hopfner KP, Eichinger A, Engh RA, Laue F, Ankenbauer W, Huber R, Angerer B
Title Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 10545321
Journal Structure Fold Des
Year 1999
Volume 7
Pages 1189-99
Authors Zhao Y, Jeruzalmi D, Moarefi I, Leighton L, Lasken R, Kuriyan J
Title Crystal structure of an archaebacterial DNA polymerase.
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Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 10860752
Journal J Mol Biol
Year 2000
Volume 299
Pages 447-62
Authors Rodriguez AC, Park HW, Mao C, Beese LS
Title Crystal structure of a pol alpha family DNA polymerase from the hyperthermophilic archaeon Thermococcus sp. 9 degrees N-7.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 11401565
Journal Biochemistry
Year 2001
Volume 40
Pages 7180-91
Authors Berdis AJ
Title Dynamics of translesion DNA synthesis catalyzed by the bacteriophage T4 exonuclease-deficient DNA polymerase.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 11504721
Journal J Biol Chem
Year 2001
Volume 276
Pages 39340-9
Authors Alley SC, Trakselis MA, Mayer MU, Ishmael FT, Jones AD, Benkovic SJ
Title Building a replisome solution structure by elucidation of protein-protein interactions in the bacteriophage T4 DNA polymerase holoenzyme.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 11178906
Journal J Mol Biol
Year 2001
Volume 306
Pages 469-77
Authors Hashimoto H, Nishioka M, Fujiwara S, Takagi M, Imanaka T, Inoue T, Kai Y
Title Crystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 11389835
Journal Cell
Year 2001
Volume 105
Pages 657-67
Authors Franklin MC, Wang J, Steitz TA
Title Structure of the replicating complex of a pol alpha family DNA polymerase.
Related PDB 1ig9 1ih7
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 12162740
Journal Biochemistry
Year 2002
Volume 41
Pages 10256-61
Authors Yang G, Franklin M, Li J, Lin TC, Konigsberg W
Title A conserved Tyr residue is required for sugar selectivity in a Pol alpha DNA polymerase.
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Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 12087102
Journal J Biol Chem
Year 2002
Volume 277
Pages 33041-8
Authors Petrov VM, Ng SS, Karam JD
Title Protein determinants of RNA binding by DNA polymerase of the T4-related bacteriophage RB69.
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Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 12415300
Journal Nat Rev Mol Cell Biol
Year 2002
Volume 3
Pages 826-35
Authors Davey MJ, Jeruzalmi D, Kuriyan J, O'Donnell M
Title Motors and switches: AAA+ machines within the replisome.
Related PDB
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID 15057283
Journal EMBO J
Year 2004
Volume 23
Pages 1483-93
Authors Hogg M, Wallace SS, Doublie S
Title Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site.
Related PDB 1rv2
Related UniProtKB
[25]
Resource
Comments
Medline ID
PubMed ID 15057282
Journal EMBO J
Year 2004
Volume 23
Pages 1494-505
Authors Freisinger E, Grollman AP, Miller H, Kisker C
Title Lesion (in)tolerance reveals insights into DNA replication fidelity.
Related PDB 1q9x 1q9y
Related UniProtKB

Comments
This enzyme belongs to the DNA polymerase type-B family.
In the CATH definition, this enzyme has got six domains. The second domain seems to have exonuclease activity, although it is not annotated in this entry. The third and fourth domains have polymerase activity.
On the third domain, two divalent metal ions such as magnesium ions and manganese ions are bound to two acidic residues. One of the metal ion, A, is bound to alpha-phosphate oxygen of deoxynucletide triphosphate (dNTP), and 3'-OH of the primer DNA. The other metal ion, B, is bound to oxgens from all three phosphate of the dNTP (see [9]).
According to the literature [9] & [11], the catalytic reaction of polymerase domains proceeds as follows:
(1) The metal ion A 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 (Arg482, Lys486, Lys560 & Asn564). According to the literature [11], Lys560 stabilizes the transferred alpha-phosphate, which is also stabilzed by both A and B metal ions. Asn564 stabilizes beta-phosphate, along with the metal ion B, Arg482 and Lys486 stabilize gamma-phosphate together with the metal ion B (see [11]). (Arg482 and Lys486 are more important than Lys560 and Asn564, according to the literature [11].)

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