PDBsum entry 3gpy

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protein dna_rna metals links
Lyase/DNA PDB id
Protein chain
273 a.a. *
Waters ×297
* Residue conservation analysis
PDB id:
Name: Lyase/DNA
Title: Sequence-matched mutm lesion recognition complex 3 (lrc3)
Structure: DNA glycosylase. Chain: a. Engineered: yes. Mutation: yes. DNA (5'-d( Ap Gp Gp Tp Ap Gp Ap Tp Cp Cp Gp Gp Ap 3'). Chain: b. Engineered: yes. DNA (5'-d( T Gp Cp Gp Tp Cp Cp (8Og)
Source: Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: mutm. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: synthetic DNA. Other_details: synthetic DNA
1.85Å     R-factor:   0.165     R-free:   0.186
Authors: Y.Qi,G.L.Verdine
Key ref: Y.Qi et al. (2009). Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme. Nature, 462, 762-766. PubMed id: 20010681
23-Mar-09     Release date:   10-Nov-09    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P84131  (P84131_GEOSE) -  Formamidopyrimidine-DNA glycosylase
274 a.a.
273 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.  - 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  


Nature 462:762-766 (2009)
PubMed id: 20010681  
Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme.
Y.Qi, M.C.Spong, K.Nam, A.Banerjee, S.Jiralerspong, M.Karplus, G.L.Verdine.
How living systems detect the presence of genotoxic damage embedded in a million-fold excess of undamaged DNA is an unresolved question in biology. Here we have captured and structurally elucidated a base-excision DNA repair enzyme, MutM, at the stage of initial encounter with a damaged nucleobase, 8-oxoguanine (oxoG), nested within a DNA duplex. Three structures of intrahelical oxoG-encounter complexes are compared with sequence-matched structures containing a normal G base in place of an oxoG lesion. Although the protein-DNA interfaces in the matched complexes differ by only two atoms-those that distinguish oxoG from G-their pronounced structural differences indicate that MutM can detect a lesion in DNA even at the earliest stages of encounter. All-atom computer simulations show the pathway by which encounter of the enzyme with the lesion causes extrusion from the DNA duplex, and they elucidate the critical free energy difference between oxoG and G along the extrusion pathway.

Literature references that cite this PDB file's key reference

  PubMed id Reference
22659876 C.Yi, B.Chen, B.Qi, W.Zhang, G.Jia, L.Zhang, C.J.Li, A.R.Dinner, C.G.Yang, and C.He (2012).
Duplex interrogation by a direct DNA repair protein in search of base damage.
  Nat Struct Mol Biol, 19, 671-676.
PDB codes: 3rzg 3rzh 3rzj 3rzk 3rzl 3rzm 3s57 3s5a
20861000 M.Firczuk, M.Wojciechowski, H.Czapinska, and M.Bochtler (2011).
DNA intercalation without flipping in the specific ThaI-DNA complex.
  Nucleic Acids Res, 39, 744-754.
PDB code: 3ndh
21068844 C.Yi, G.Jia, G.Hou, Q.Dai, W.Zhang, G.Zheng, X.Jian, C.G.Yang, Q.Cui, and C.He (2010).
Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase.
  Nature, 468, 330-333.
PDB codes: 3o1m 3o1o 3o1p 3o1r 3o1s 3o1t 3o1u 3o1v
20118965 G.M.Li (2010).
Novel molecular insights into the mechanism of GO removal by MutM.
  Cell Res, 20, 116-118.  
21070960 R.P.Rambo, G.J.Williams, and J.A.Tainer (2010).
Achieving fidelity in homologous recombination despite extreme complexity: informed decisions by molecular profiling.
  Mol Cell, 40, 347-348.  
19889642 Y.Qi, M.C.Spong, K.Nam, M.Karplus, and G.L.Verdine (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.
PDB codes: 3jr4 3jr5
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