PDBsum entry 4g4r

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protein dna_rna metals links
Hydrolase/DNA PDB id
Protein chain
252 a.a.
Waters ×198
PDB id:
Name: Hydrolase/DNA
Title: Mutm containing f114a mutation bound to oxog-containing DNA
Structure: Formamidopyrimidine-DNA glycosylase. Chain: a. Fragment: mutm. Synonym: fapy-DNA glycosylase, DNA-(apurinic or apyrimidini lyase mutm. Engineered: yes. Mutation: yes. DNA (5'- d(p Ap Gp Gp Tp Ap Gp Ap Cp Tp Cp Gp Gp Ap Cp Gp C)-3').
Source: Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: mutm. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes
1.95Å     R-factor:   0.174     R-free:   0.214
Authors: R.J.Sung,M.Zhang,Y.Qi,G.L.Verdine
Key ref: R.J.Sung et al. (2013). Structural and biochemical analysis of DNA helix invasion by the bacterial 8-oxoguanine DNA glycosylase MutM. J Biol Chem, 288, 10012-10023. PubMed id: 23404556 DOI: 10.1074/jbc.M112.415612
16-Jul-12     Release date:   20-Feb-13    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P84131  (P84131_GEOSE) -  Formamidopyrimidine-DNA glycosylase
274 a.a.
252 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: 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.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   6 terms 
  Biochemical function     catalytic activity     12 terms  


DOI no: 10.1074/jbc.M112.415612 J Biol Chem 288:10012-10023 (2013)
PubMed id: 23404556  
Structural and biochemical analysis of DNA helix invasion by the bacterial 8-oxoguanine DNA glycosylase MutM.
R.J.Sung, M.Zhang, Y.Qi, G.L.Verdine.
MutM is a bacterial DNA glycosylase that serves as the first line of defense against the highly mutagenic 8-oxoguanine (oxoG) lesion, catalyzing glycosidic bond cleavage of oxoG to initiate base excision DNA repair. Previous work has shown that MutM actively interrogates DNA for the presence of an intrahelical oxoG lesion. This interrogation process involves significant buckling and bending of the DNA to promote extrusion of oxoG from the duplex. Structural snapshots have revealed several different highly conserved residues that are prominently inserted into the duplex in the vicinity of the target oxoG before and after base extrusion has occurred. However, the roles of these helix-invading residues during the lesion recognition and base extrusion process remain unclear. In this study, we set out to probe the function of residues Phe(114) and Met(77) in oxoG recognition and repair. Here we report a detailed biochemical and structural characterization of MutM variants containing either a F114A or M77A mutation, both of which showed significant decreases in the efficiency of oxoG repair. These data reveal that Met(77) plays an important role in stabilizing the lesion-extruded conformation of the DNA. Phe(114), on the other hand, appears to destabilize the intrahelical state of the oxoG lesion, primarily by buckling the target base pair. We report the observation of a completely unexpected interaction state, in which the target base pair is ruptured but remains fully intrahelical; this structure vividly illustrates the disruptive influence of MutM on the target base pair.