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RB69 DNA Polymerase Ternary Complex with dCTP Opposite an Abasic Site and ddG/dC as the Penultimate Base-pair

Source organism: Escherichia phage RB69
Biochemical function: metal ion binding
Biological process: DNA replication proofreading
Cellular component: not assigned

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EC 2.7.7.7: DNA-directed DNA polymerase

Reaction catalysed:
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Systematic name:
Deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (DNA-directed)
Alternative Name(s):
  • DNA duplicase
  • DNA nucleotidyltransferase
  • DNA nucleotidyltransferase (DNA-directed)
  • DNA polymerase
  • DNA polymerase I
  • DNA polymerase II
  • DNA polymerase III
  • DNA polymerase alpha
  • DNA polymerase beta
  • DNA polymerase gamma
  • DNA replicase
  • DNA-dependent DNA polymerase
  • Deoxynucleate polymerase
  • Deoxyribonucleate nucleotidyltransferase
  • Deoxyribonucleic acid duplicase
  • Deoxyribonucleic acid polymerase
  • Deoxyribonucleic duplicase
  • Deoxyribonucleic polymerase
  • Deoxyribonucleic polymerase I
  • Duplicase
  • Klenow fragment
  • Sequenase
  • Taq DNA polymerase
  • Taq Pol I
  • Tca DNA polymerase

GO terms

Sequence families

Pfam Protein families (Pfam)
PF00136
Domain description: DNA polymerase family B
Occurring in:
  1. DNA-directed DNA polymerase
The deposited structure of PDB entry 4dtm contains 2 copies of Pfam domain PF00136 (DNA polymerase family B) in DNA-directed DNA polymerase. Showing 2 copies in chain A.

PF03104
Domain description: DNA polymerase family B, exonuclease domain
Occurring in:
  1. DNA-directed DNA polymerase
The deposited structure of PDB entry 4dtm contains 1 copy of Pfam domain PF03104 (DNA polymerase family B, exonuclease domain) in DNA-directed DNA polymerase. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR006172
Domain description: DNA-directed DNA polymerase, family B
Occurring in:
  1. DNA-directed DNA polymerase
IPR017964
Domain description: DNA-directed DNA polymerase, family B, conserved site
Occurring in:
  1. DNA-directed DNA polymerase
IPR023211
Domain description: DNA polymerase, palm domain superfamily
Occurring in:
  1. DNA-directed DNA polymerase
IPR043502
Domain description: DNA/RNA polymerase superfamily
Occurring in:
  1. DNA-directed DNA polymerase
IPR006134
Domain description: DNA-directed DNA polymerase, family B, multifunctional domain
Occurring in:
  1. DNA-directed DNA polymerase
IPR036397
Domain description: Ribonuclease H superfamily
Occurring in:
  1. DNA-directed DNA polymerase
IPR006133
Domain description: DNA-directed DNA polymerase, family B, exonuclease domain
Occurring in:
  1. DNA-directed DNA polymerase
IPR012337
Domain description: Ribonuclease H-like superfamily
Occurring in:
  1. DNA-directed DNA polymerase
IPR034749
Domain description: DNA-directed DNA polymerase T4 type
Occurring in:
  1. DNA-directed DNA polymerase

Structure domains

CATH CATH domains
1.20.1280.300
Class: Mainly Alpha
Architecture: Up-down Bundle
Topology: Monooxygenase
Homology: Monooxygenase
Occurring in:
  1. DNA-directed DNA polymerase
The deposited structure of PDB entry 4dtm contains 1 copy of CATH domain 1.20.1280.300 (Monooxygenase) in DNA-directed DNA polymerase. Showing 1 copy in chain A.
3.90.1600.10
Class: Alpha Beta
Architecture: Alpha-Beta Complex
Topology: Palm domain of DNA polymerase
Homology: Palm domain of DNA polymerase
Occurring in:
  1. DNA-directed DNA polymerase
The deposited structure of PDB entry 4dtm contains 1 copy of CATH domain 3.90.1600.10 (Palm domain of DNA polymerase) in DNA-directed DNA polymerase. Showing 1 copy in chain A.
3.30.342.10
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: DNA Polymerase; Chain A, domain 1
Homology: DNA Polymerase, chain B, domain 1
Occurring in:
  1. DNA-directed DNA polymerase
The deposited structure of PDB entry 4dtm contains 1 copy of CATH domain 3.30.342.10 (DNA Polymerase; Chain A, domain 1) in DNA-directed DNA polymerase. Showing 1 copy in chain A.
3.40.1820.10
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Ribonuclease H-like motif
Homology: DnaQ-like 3'-5' exonuclease
Occurring in:
  1. DNA-directed DNA polymerase
The deposited structure of PDB entry 4dtm contains 1 copy of CATH domain 3.40.1820.10 (Ribonuclease H-like motif) in DNA-directed DNA polymerase. Showing 1 copy in chain A.
1.10.287.690
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Helix Hairpins
Homology: Helix hairpin bin
Occurring in:
  1. DNA-directed DNA polymerase
The deposited structure of PDB entry 4dtm contains 1 copy of CATH domain 1.10.287.690 (Helix Hairpins) in DNA-directed DNA polymerase. Showing 1 copy in chain A.
3.30.420.10
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Nucleotidyltransferase; domain 5
Homology: Ribonuclease H-like superfamily/Ribonuclease H
Occurring in:
  1. DNA-directed DNA polymerase
The deposited structure of PDB entry 4dtm contains 1 copy of CATH domain 3.30.420.10 (Nucleotidyltransferase; domain 5) in DNA-directed DNA polymerase. Showing 1 copy in chain A.

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