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Crystal Structure of Bacillus DNA Polymerase I Fragment complexed to 9 base pairs of duplex DNA.

Source organism: Geobacillus stearothermophilus
Biochemical function: 3'-5' exonuclease activity
Biological process: DNA-templated DNA replication
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 family

Pfam Protein family (Pfam)
PF00476
Domain description: DNA polymerase family A
Occurring in:
  1. DNA polymerase I
The deposited structure of PDB entry 1l3s contains 1 copy of Pfam domain PF00476 (DNA polymerase family A) in DNA polymerase I. Showing 1 copy in chain C [auth A].

InterPro InterPro annotations
IPR002298
Domain description: DNA polymerase A
Occurring in:
  1. DNA polymerase I
IPR001098
Domain description: DNA-directed DNA polymerase, family A, palm domain
Occurring in:
  1. DNA polymerase I
IPR019760
Domain description: DNA-directed DNA polymerase, family A, conserved site
Occurring in:
  1. DNA polymerase I
IPR043502
Domain description: DNA/RNA polymerase superfamily
Occurring in:
  1. DNA polymerase I
IPR018320
Domain description: DNA polymerase 1
Occurring in:
  1. DNA polymerase I
IPR012337
Domain description: Ribonuclease H-like superfamily
Occurring in:
  1. DNA polymerase I
IPR002562
Domain description: 3'-5' exonuclease domain
Occurring in:
  1. DNA polymerase I
IPR036397
Domain description: Ribonuclease H superfamily
Occurring in:
  1. DNA polymerase I

Structure domains

CATH CATH domains
3.30.70.370
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Alpha-Beta Plaits
Homology: Alpha-Beta Plaits
Occurring in:
  1. DNA polymerase I
The deposited structure of PDB entry 1l3s contains 1 copy of CATH domain 3.30.70.370 (Alpha-Beta Plaits) in DNA polymerase I. Showing 1 copy in chain C [auth A].
1.10.150.20
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: DNA polymerase; domain 1
Homology: 5' to 3' exonuclease, C-terminal subdomain
Occurring in:
  1. DNA polymerase I
The deposited structure of PDB entry 1l3s contains 1 copy of CATH domain 1.10.150.20 (DNA polymerase; domain 1) in DNA polymerase I. Showing 1 copy in chain C [auth A].
1.20.1060.10
Class: Mainly Alpha
Architecture: Up-down Bundle
Topology: Taq DNA Polymerase; Chain T, domain 4
Homology: Taq DNA Polymerase; Chain T, domain 4
Occurring in:
  1. DNA polymerase I
The deposited structure of PDB entry 1l3s contains 1 copy of CATH domain 1.20.1060.10 (Taq DNA Polymerase; Chain T, domain 4) in DNA polymerase I. Showing 1 copy in chain C [auth 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 polymerase I
The deposited structure of PDB entry 1l3s contains 1 copy of CATH domain 3.30.420.10 (Nucleotidyltransferase; domain 5) in DNA polymerase I. Showing 1 copy in chain C [auth A].
SCOP SCOP annotations
56673
Class: Multi-domain proteins (alpha and beta)
Fold: DNA/RNA polymerases
Superfamily: DNA/RNA polymerases
Occurring in:
  1. DNA polymerase I
The deposited structure of PDB entry 1l3s contains 1 copy of SCOP domain 56673 (DNA polymerase I) in DNA polymerase I. Showing 1 copy in chain C [auth A].
53118
Class: Alpha and beta proteins (a/b)
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Occurring in:
  1. DNA polymerase I
The deposited structure of PDB entry 1l3s contains 1 copy of SCOP domain 53118 (DnaQ-like 3'-5' exonuclease) in DNA polymerase I. Showing 1 copy in chain C [auth A].

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