Function and Biology

Crystal Structure of Lactococcus lactis Formamido-pyrimidine DNA Glycosylase (alias Fpg or MutM) Non Covalently Bound to an AP Site Containing DNA.

Source organisms:
Biochemical function: class III/IV DNA-(apurinic or apyrimidinic site) lyase activity
Biological process: nucleotide-excision repair
Cellular component: not assigned

EC 3.2.2.23: DNA-formamidopyrimidine glycosylase

Reaction catalysed:
Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine.
Comments:
  • May play a significant role in processes leading to recovery from mutagenesis and/or cell death by alkylating agents.
  • Also involved in the GO system responsible for removing an oxidatively damaged form of guanine (7,8-dihydro-8-oxoguanine) from DNA.
Systematic name:
DNA glycohydrolase (2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimide releasing)
Alternative Name(s):
  • 2,6-diamino-4-hydroxy-5(N-methyl)formamidopyrimidine-DNA glycosylase
  • 2,6-diamino-4-hydroxy-5N-formamidopyrimidine-DNA glycosylase
  • Fapy-DNA glycosylase
  • Fpg protein
  • Deoxyribonucleate glycosidase
  • Formamidopyrimidine-DNA glycosylase

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.
Comments:
  • 'Nicking' of the phosphodiester bond is due to a lyase-type reaction, not hydrolysis.
  • This group of enzymes was previously listed as endonucleases, under the number EC 3.1.25.2.
Systematic name:
DNA-(apurinic or apyrimidinic site) 5'-phosphomonoester-lyase
Alternative Name(s):
  • E. coli endonuclease III
  • Micrococcus luteus UV endonuclease
  • AP endonuclease class I
  • AP lyase
  • AP site-DNA 5'-phosphomonoester-lyase
  • X-ray endonuclease III
  • Deoxyribonuclease (apurinic or apyrimidinic)
  • Endodeoxyribonuclease (apurinic or apyrimidinic)
  • Phage-T(4) UV endonuclease
  • Phage-T4 UV endonuclease
  • E.coli endonuclease III

Sequence family

Pfam Protein family (Pfam)
PF06827
Domain description: Zinc finger found in FPG and IleRS
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase
1 copy of Pfam domain PF06827 (Zinc finger found in FPG and IleRS) in Formamidopyrimidine-DNA glycosylase in PDB 1kfv.

InterPro InterPro annotations
IPR012319
Domain description: Formamidopyrimidine-DNA glycosylase, catalytic domain
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase
IPR015886
Domain description: DNA glycosylase/AP lyase, H2TH DNA-binding
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase
IPR020629
Domain description: Formamidopyrimidine-DNA glycosylase
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase
IPR035937
Domain description: MutM-like, N-terminal
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase
IPR000214
Domain description: Zinc finger, DNA glycosylase/AP lyase-type
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase
IPR010663
Domain description: Zinc finger, FPG/IleRS-type
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase
IPR015887
Domain description: DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase
IPR010979
Domain description: Ribosomal protein S13-like, H2TH
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase

Structure domains

CATH CATH domains
3.20.190.10
Class: Alpha Beta
Architecture: Alpha-Beta Barrel
Topology: N-terminal domain of MutM-like DNA repair proteins
Homology: N-terminal domain of MutM-like DNA repair proteins
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase
1 copy of CATH domain 3.20.190.10 (N-terminal domain of MutM-like DNA repair proteins) in Formamidopyrimidine-DNA glycosylase in PDB 1kfv.
1.10.8.50
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Helicase, Ruva Protein; domain 3
Homology: Helicase, Ruva Protein; domain 3
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase
1 copy of CATH domain 1.10.8.50 (Helicase, Ruva Protein; domain 3) in Formamidopyrimidine-DNA glycosylase in PDB 1kfv.
SCOP SCOP annotations
81626
Class: All alpha proteins
Fold: S13-like H2TH domain
Superfamily: S13-like H2TH domain
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase
1 copy of SCOP domain 81626 (Middle domain of MutM-like DNA repair proteins) in Formamidopyrimidine-DNA glycosylase in PDB 1kfv.
81627
Class: Small proteins
Fold: Glucocorticoid receptor-like (DNA-binding domain)
Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase
1 copy of SCOP domain 81627 (C-terminal, Zn-finger domain of MutM-like DNA repair proteins) in Formamidopyrimidine-DNA glycosylase in PDB 1kfv.
81623
Class: All beta proteins
Fold: N-terminal domain of MutM-like DNA repair proteins
Superfamily: N-terminal domain of MutM-like DNA repair proteins
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase
1 copy of SCOP domain 81623 (N-terminal domain of MutM-like DNA repair proteins) in Formamidopyrimidine-DNA glycosylase in PDB 1kfv.