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ATOMIC MODEL OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME COMPLEXED WITH A DNA SUBSTRATE: STRUCTURAL BASIS FOR DAMAGED DNA RECOGNITION

Source organism: Tequatrovirus T4
Biochemical function: class I DNA-(apurinic or apyrimidinic site) endonuclease activity
Biological process: DNA repair
Cellular component: not assigned

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EC 4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase

Reaction catalysed:
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Systematic name:
DNA-(apurinic or apyrimidinic site) 5'-phosphomonoester-lyase
Alternative Name(s):
  • AP endonuclease class I
  • AP lyase
  • AP site-DNA 5'-phosphomonoester-lyase
  • Deoxyribonuclease (apurinic or apyrimidinic)
  • E. coli endonuclease III
  • E.coli endonuclease III
  • Endodeoxyribonuclease (apurinic or apyrimidinic)
  • Micrococcus luteus UV endonuclease
  • Phage-T(4) UV endonuclease
  • Phage-T4 UV endonuclease
  • X-ray endonuclease III

EC 3.2.2.17: Deoxyribodipyrimidine endonucleosidase

Reaction catalysed:
Cleaves the N-glycosidic bond between the 5'-pyrimidine residue in cyclobutadipyrimidine (in DNA) and the corresponding deoxy-D-ribose residue
Systematic name:
Deoxy-D-ribocyclobutadipyrimidine polynucleotidodeoxyribohydrolase
Alternative Name(s):
  • Deoxyribonucleate pyrimidine dimer glycosidase
  • Endonuclease V
  • PD-DNA glycosylase
  • Pyrimidine dimer DNA glycosylase
  • Pyrimidine dimer DNA-glycosylase
  • T4-induced UV endonuclease

GO terms

Sequence family

Pfam Protein family (Pfam)
PF03013
Domain description: Pyrimidine dimer DNA glycosylase
Occurring in:
  1. Endonuclease V
The deposited structure of PDB entry 1vas contains 1 copy of Pfam domain PF03013 (Pyrimidine dimer DNA glycosylase) in Endonuclease V. Showing 1 copy in chain C [auth A].

InterPro InterPro annotations
IPR004260
Domain description: Pyrimidine dimer DNA glycosylase
Occurring in:
  1. Endonuclease V
IPR024796
Domain description: T4 endonuclease V
Occurring in:
  1. Endonuclease V
IPR021143
Domain description: Pyrimidine dimer DNA glycosylase, endonuclease V type
Occurring in:
  1. Endonuclease V

Structure domain

CATH CATH domain
1.10.440.10
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Endonuclease V
Homology: T4 endonuclease V
Occurring in:
  1. Endonuclease V
The deposited structure of PDB entry 1vas contains 1 copy of CATH domain 1.10.440.10 (Endonuclease V) in Endonuclease V. Showing 1 copy in chain C [auth A].
SCOP SCOP annotation
47078
Class: All alpha proteins
Fold: T4 endonuclease V
Superfamily: T4 endonuclease V
Occurring in:
  1. Endonuclease V
The deposited structure of PDB entry 1vas contains 1 copy of SCOP domain 47078 (T4 endonuclease V) in Endonuclease V. Showing 1 copy in chain C [auth A].

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