PDBsum entry 3c58

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protein dna_rna ligands metals links
Hydrolase/DNA PDB id
Protein chain
269 a.a. *
Waters ×335
* Residue conservation analysis
PDB id:
Name: Hydrolase/DNA
Title: Crystal structure of a complex between the wild-type lactoco lactis fpg (mutm) and a n7-benzyl-fapy-dg containing DNA
Structure: DNA glycosylase. Chain: a. Synonym: fapy-DNA glycosylase, DNA-apurinic or apyrimidinic lyase mutm, ap lyase mutm. Engineered: yes. DNA (5'-d( Dcp Dtp Dcp Dtp Dtp Dtp (Sos) p Dtp Dtp Dtp Dcp Dtp Dcp Dg)-3'). Chain: b. Engineered: yes.
Source: Lactococcus lactis. Organism_taxid: 416870. Variant: subsp. Cremoris. Gene: mutm, fpg. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: synthetic DNA. Other_details: synthetic DNA
1.90Å     R-factor:   0.173     R-free:   0.200
Authors: F.Coste,B.Castaing,T.Carell
Key ref: F.Coste et al. (2008). Bacterial base excision repair enzyme Fpg recognizes bulky N7-substituted-FapydG lesion via unproductive binding mode. Chem Biol, 15, 706-717. PubMed id: 18635007
31-Jan-08     Release date:   16-Dec-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P42371  (FPG_LACLC) -  Formamidopyrimidine-DNA glycosylase
273 a.a.
269 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 1: E.C.  - DNA-formamidopyrimidine glycosylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of DNA containing ring-opened N(7)-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimide.
   Enzyme class 2: E.C.  - DNA-(apurinic or apyrimidinic site) lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 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.
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   6 terms 
  Biochemical function     catalytic activity     12 terms  


Chem Biol 15:706-717 (2008)
PubMed id: 18635007  
Bacterial base excision repair enzyme Fpg recognizes bulky N7-substituted-FapydG lesion via unproductive binding mode.
F.Coste, M.Ober, Y.V.Le Bihan, M.A.Izquierdo, N.Hervouet, H.Mueller, T.Carell, B.Castaing.
Fpg is a bacterial base excision repair enzyme that removes oxidized purines from DNA. This work shows that Fpg and its eukaryote homolog Ogg1 recognize with high affinity FapydG and bulky N7-benzyl-FapydG (Bz-FapydG). The comparative crystal structure analysis of stable complexes between Fpg and carbocyclic cFapydG or Bz-cFapydG nucleoside-containing DNA provides the molecular basis of the ability of Fpg to bind both lesions with the same affinity and to differently process them. To accommodate the steric hindrance of the benzyl group, Fpg selects the adequate rotamer of the extrahelical Bz-cFapydG formamido group, forcing the bulky group to go outside the binding pocket. Contrary to the binding mode of cFapydG, the particular recognition of Bz-cFapydG leads the BER enzymes to unproductive complexes which would hide the lesion and slow down its repair by the NER machinery.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20540060 M.Winnacker, V.Welzmiller, R.Strasser, and T.Carell (2010).
Development of a DNA photoaffinity probe for the analysis of 8-OxodG-binding proteins in a human proteome.
  Chembiochem, 11, 1345-1349.  
19625256 K.Imamura, S.S.Wallace, and S.Doublié (2009).
Structural characterization of a viral NEIL1 ortholog unliganded and bound to abasic site-containing DNA.
  J Biol Chem, 284, 26174-26183.
PDB codes: 3a42 3a45 3a46
19258314 S.Couvé, G.Macé-Aimé, F.Rosselli, and M.K.Saparbaev (2009).
The Human Oxidative DNA Glycosylase NEIL1 Excises Psoralen-induced Interstrand DNA Cross-links in a Three-stranded DNA Structure.
  J Biol Chem, 284, 11963-11970.  
19200715 S.Schneider, S.Schorr, and T.Carell (2009).
Crystal structure analysis of DNA lesion repair and tolerance mechanisms.
  Curr Opin Struct Biol, 19, 87-95.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.