Function and Biology

CRYSTAL STRUCTURE OF ESCHERICHIA COLI ENDONUCLEASE IV IN COMPLEX WITH DAMAGED DNA

Source organisms:
Biochemical function: zinc ion binding
Biological process: non-recombinational repair
Cellular component: not assigned

EC 3.1.21.2: Deoxyribonuclease IV

Reaction catalysed:
Endonucleolytic cleavage to 5'-phosphooligonucleotide end-products.
Comments:
  • The enzyme is an apurinic/apyrimidinic (AP) site endonuclease that primes DNA repair synthesis at AP sites.
  • It specifically cleaves the DNA backbone at AP sites and also removes 3' DNA-blocking groups such as 3' phosphates, 3' phosphoglycolates, and 3' alpha,beta-unsaturated aldehydes that arise from oxidative base damage and the activity of combined glycosylase/lyase enzymes.
  • It is also the only known repair enzyme that is able to cleave the DNA backbone 5' of the oxidative lesion alpha-deoxyadenosine.
  • The enzyme has a strong preference for single-stranded DNA.
  • Formerly EC 3.1.4.30.
Systematic name:
-
Alternative Name(s):
  • E. coli endonuclease IV
  • Escherichia coli endonuclease II
  • DNA-adenine-transferase
  • Deoxriboendonuclease
  • Endodeoxyribonuclease
  • Endodeoxyribonuclease IV (phage T(4)-induced)
  • Endonuclease II
  • Redoxyendonuclease
  • Endodeoxyribonuclease IV (phage T4-induced)
  • Endonuclease IV
  • Deoxyribonuclease IV (phage T4-induced)
  • Nfo (gene name)

Sequence family

Pfam Protein family (Pfam)
PF01261
Domain description: Xylose isomerase-like TIM barrel
Occurring in:
  1. Endonuclease 4
1 copy of Pfam domain PF01261 (Xylose isomerase-like TIM barrel) in Endonuclease 4 in PDB 1qum.

InterPro InterPro annotations
IPR001719
Domain description: AP endonuclease 2
Occurring in:
  1. Endonuclease 4
IPR018246
Domain description: AP endonuclease 2, zinc binding site
Occurring in:
  1. Endonuclease 4
IPR013022
Domain description: Xylose isomerase-like, TIM barrel domain
Occurring in:
  1. Endonuclease 4
IPR036237
Domain description: Xylose isomerase-like superfamily
Occurring in:
  1. Endonuclease 4

Structure domain

CATH CATH domain
3.20.20.150
Class: Alpha Beta
Architecture: Alpha-Beta Barrel
Topology: TIM Barrel
Homology: Divalent-metal-dependent TIM barrel enzymes
Occurring in:
  1. Endonuclease 4
1 copy of CATH domain 3.20.20.150 (TIM Barrel) in Endonuclease 4 in PDB 1qum.
SCOP SCOP annotation
51659
Class: Alpha and beta proteins (a/b)
Fold: TIM beta/alpha-barrel
Superfamily: Xylose isomerase-like
Occurring in:
  1. Endonuclease 4
1 copy of SCOP domain 51659 (Endonuclease IV) in Endonuclease 4 in PDB 1qum.