PDBsum entry 1pjj

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protein dna_rna ligands metals links
Hydrolase/DNA PDB id
Protein chain
271 a.a. *
GOL ×3
Waters ×278
* Residue conservation analysis
PDB id:
Name: Hydrolase/DNA
Title: Complex between the lactococcus lactis fpg and an abasic sit containing DNA.
Structure: DNA (5'-d( Cp Tp Cp Tp Tp Tp (3Dr)p Tp Tp Tp Cp T 3'). Chain: d. Engineered: yes. DNA (5'-d( Gp Cp Gp Ap Gp Ap Ap Ap Cp Ap Ap Ap Gp chain: e. Engineered: yes. Formamidopyrimidine-DNA glycosylase. Chain: a.
Source: Synthetic: yes. Lactococcus lactis. Organism_taxid: 1358. Gene: mutm or fpg. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
1.90Å     R-factor:   0.202     R-free:   0.220
Authors: L.Serre,K.Pereira De Jesus,S.Boiteux,C.Zelwer,B.Castaing
Key ref: K.Pereira de Jésus et al. (2005). Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA. Nucleic Acids Res, 33, 5936-5944. PubMed id: 16243784
03-Jun-03     Release date:   08-Jun-04    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P42371  (FPG_LACLC) -  Formamidopyrimidine-DNA glycosylase
273 a.a.
271 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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  


Nucleic Acids Res 33:5936-5944 (2005)
PubMed id: 16243784  
Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA.
K.Pereira de Jésus, L.Serre, C.Zelwer, B.Castaing.
Fpg is a DNA glycosylase that recognizes and excises the mutagenic 8-oxoguanine (8-oxoG) and the potentially lethal formamidopyrimidic residues (Fapy). Fpg is also associated with an AP lyase activity which successively cleaves the abasic (AP) site at the 3' and 5' sides by betadelta-elimination. Here, we present the high-resolution crystal structures of the wild-type and the P1G defective mutant of Fpg from Lactococcus lactis bound to 14mer DNA duplexes containing either a tetrahydrofuran (THF) or 1,3-propanediol (Pr) AP site analogues. Structures show that THF is less extrahelical than Pr and its backbone C5'-C4'-C3' diverges significantly from those of Pr, rAP, 8-oxodG and FapydG. Clearly, the heterocyclic oxygen of THF is pushed back by the carboxylate of the strictly conserved E2 residue. We can propose that the ring-opened form of the damaged deoxyribose is the structure active form of the sugar for Fpg catalysis process. Both structural and functional data suggest that the first step of catalysis mediated by Fpg involves the expulsion of the O4' leaving group facilitated by general acid catalysis (involving E2), rather than the immediate cleavage of the N-glycosic bond of the damaged nucleoside.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19304747 G.Sicoli, G.Mathis, S.Aci-Sèche, C.Saint-Pierre, Y.Boulard, D.Gasparutto, and S.Gambarelli (2009).
Lesion-induced DNA weak structural changes detected by pulsed EPR spectroscopy combined with site-directed spin labelling.
  Nucleic Acids Res, 37, 3165-3176.  
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
18635007 F.Coste, M.Ober, Y.V.Le Bihan, M.A.Izquierdo, N.Hervouet, H.Mueller, T.Carell, and B.Castaing (2008).
Bacterial base excision repair enzyme Fpg recognizes bulky N7-substituted-FapydG lesion via unproductive binding mode.
  Chem Biol, 15, 706-717.
PDB code: 3c58
18506863 H.Mueller, M.Hopfinger, and T.Carell (2008).
Synthesis of a stabilized version of the imidazolone DNA lesion.
  Chembiochem, 9, 1617-1622.  
17432829 L.Jia, V.Shafirovich, N.E.Geacintov, and S.Broyde (2007).
Lesion specificity in the base excision repair enzyme hNeil1: modeling and dynamics studies.
  Biochemistry, 46, 5305-5314.  
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