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Crystal Structure Complex Between the Lactococcus Lactis FPG (Mutm) and a FAPY-dG Containing DNA

Source organism: Lactococcus lactis
Biochemical function: class I DNA-(apurinic or apyrimidinic site) endonuclease activity
Biological process: metabolic process
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 3.2.2.23: DNA-formamidopyrimidine glycosylase

Reaction catalysed:
Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine
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
  • Deoxyribonucleate glycosidase
  • Fapy-DNA glycosylase
  • Formamidopyrimidine-DNA glycosylase
  • Fpg protein

GO terms

Sequence families

Pfam Protein families (Pfam)
PF06827
Domain description: Zinc finger found in FPG and IleRS
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase
The deposited structure of PDB entry 1tdz contains 1 copy of Pfam domain PF06827 (Zinc finger found in FPG and IleRS) in Formamidopyrimidine-DNA glycosylase. Showing 1 copy in chain C [auth A].

PF06831
Domain description: Formamidopyrimidine-DNA glycosylase H2TH domain
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase
The deposited structure of PDB entry 1tdz contains 1 copy of Pfam domain PF06831 (Formamidopyrimidine-DNA glycosylase H2TH domain) in Formamidopyrimidine-DNA glycosylase. Showing 1 copy in chain C [auth A].

PF01149
Domain description: Formamidopyrimidine-DNA glycosylase N-terminal domain
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase
The deposited structure of PDB entry 1tdz contains 1 copy of Pfam domain PF01149 (Formamidopyrimidine-DNA glycosylase N-terminal domain) in Formamidopyrimidine-DNA glycosylase. Showing 1 copy in chain C [auth A].

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
IPR035937
Domain description: MutM-like, N-terminal
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase
IPR020629
Domain description: Formamidopyrimidine-DNA glycosylase
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
IPR010663
Domain description: Zinc finger, FPG/IleRS-type
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase
IPR000214
Domain description: Zinc finger, DNA glycosylase/AP lyase-type
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase
IPR010979
Domain description: Small ribosomal subunit protein uS13-like, H2TH
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase

Structure domains

CATH CATH domains
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
The deposited structure of PDB entry 1tdz contains 1 copy of CATH domain 1.10.8.50 (Helicase, Ruva Protein; domain 3) in Formamidopyrimidine-DNA glycosylase. Showing 1 copy in chain C [auth A].
3.20.190.10
Class: Alpha Beta
Architecture: Alpha-Beta Barrel
Topology: N-terminal domain of MutM-like DNA repair proteins
Homology: MutM-like, N-terminal
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase
The deposited structure of PDB entry 1tdz contains 1 copy of CATH domain 3.20.190.10 (N-terminal domain of MutM-like DNA repair proteins) in Formamidopyrimidine-DNA glycosylase. Showing 1 copy in chain C [auth A].
SCOP SCOP annotations
81627
Class: Small proteins
Fold: Glucocorticoid receptor-like (DNA-binding domain)
Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase
The deposited structure of PDB entry 1tdz contains 1 copy of SCOP domain 81627 (C-terminal, Zn-finger domain of MutM-like DNA repair proteins) in Formamidopyrimidine-DNA glycosylase. Showing 1 copy in chain C [auth A].
81626
Class: All alpha proteins
Fold: S13-like H2TH domain
Superfamily: S13-like H2TH domain
Occurring in:
  1. Formamidopyrimidine-DNA glycosylase
The deposited structure of PDB entry 1tdz contains 1 copy of SCOP domain 81626 (Middle domain of MutM-like DNA repair proteins) in Formamidopyrimidine-DNA glycosylase. Showing 1 copy in chain C [auth A].
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
The deposited structure of PDB entry 1tdz contains 1 copy of SCOP domain 81623 (N-terminal domain of MutM-like DNA repair proteins) in Formamidopyrimidine-DNA glycosylase. Showing 1 copy in chain C [auth A].

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