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PDBsum entry 3jr4

Go to PDB code: 
protein dna_rna metals links
Lyase/DNA PDB id
3jr4
Jmol
Contents
Protein chain
263 a.a. *
DNA/RNA
Metals
_ZN
Waters ×64
* Residue conservation analysis
PDB id:
3jr4
Name: Lyase/DNA
Title: Mutm interrogating an extrahelical g
Structure: DNA glycosylase. Chain: a. Fragment: mutm. Engineered: yes. Mutation: yes. DNA (5'- d( Ap Gp Gp Tp Ap Gp Ap Cp Cp Tp Gp Gp Ap Cp Gp C)-3'). Chain: b. Engineered: yes.
Source: Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: mutm. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes
Resolution:
2.60Å     R-factor:   0.193     R-free:   0.237
Authors: Y.Qi,M.C.Spong,G.L.Verdine
Key ref:
Y.Qi et al. (2010). Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM. J Biol Chem, 285, 1468-1478. PubMed id: 19889642 DOI: 10.1074/jbc.M109.069799
Date:
08-Sep-09     Release date:   03-Nov-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P84131  (P84131_GEOSE) -  Formamidopyrimidine-DNA glycosylase
Seq:
Struc:
274 a.a.
263 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.2.2.23  - 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.M109.069799 J Biol Chem 285:1468-1478 (2010)
PubMed id: 19889642  
 
 
Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM.
Y.Qi, M.C.Spong, K.Nam, M.Karplus, G.L.Verdine.
 
  ABSTRACT  
 
MutM, a bacterial DNA glycosylase, protects genome integrity by catalyzing glycosidic bond cleavage of 8-oxoguanine (oxoG) lesions, thereby initiating base excision DNA repair. The process of searching for and locating oxoG lesions is especially challenging, because of the close structural resemblance of oxoG to its million-fold more abundant progenitor, G. Extrusion of the target nucleobase from the DNA double helix to an extrahelical position is an essential step in lesion recognition and catalysis by MutM. Although the interactions between the extruded oxoG and the active site of MutM have been well characterized, little is known in structural detail regarding the interrogation of extruded normal DNA bases by MutM. Here we report the capture and structural elucidation of a complex in which MutM is attempting to present an undamaged G to its active site. The structure of this MutM-extrahelical G complex provides insights into the mechanism MutM employs to discriminate against extrahelical normal DNA bases and into the base extrusion process in general.
 
  Selected figure(s)  
 
Figure 1.
A, oxidation of G by reactive oxygen species (ROS) generates oxoG. The differences between oxoG and G are highlighted in yellow. B, schematics of four major MutM-DNA interaction stages along the base extrusion pathway. Acronyms of the crystal structures (see text) are shown under the corresponding stages, and the newly captured state is highlighted with a yellow background.
Figure 4.
Comparison of the DNA backbone conformations. A, LRC[N174C] (blue) and the un-cross-linked LRC[1R2Y] (wheat). B, LRC[N174C] (blue) and XGC (light blue). The cross-link (purple) and the target base (red for oxoG and blue for G) are shown in ball-and-stick. Major conformational differences are denoted with black arrows. Only the helix in MutM containing the cross-linking site N174C is shown for each complex. The right panels show close-up views of the DNA strands bearing the target nucleobase.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2010, 285, 1468-1478) copyright 2010.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20118965 G.M.Li (2010).
Novel molecular insights into the mechanism of GO removal by MutM.
  Cell Res, 20, 116-118.  
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.

 

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