PDBsum entry 1m3h

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protein dna_rna metals links
Hydrolase/DNA PDB id
Protein chain
314 a.a. *
Waters ×92
* Residue conservation analysis
PDB id:
Name: Hydrolase/DNA
Title: Crystal structure of hogg1 d268e mutant with product oligonucleotide
Structure: 5'- d(p Gp Gp Tp Ap Gp Ap Cp Cp Tp Gp Gp Ap Cp Gp C)-3'. Chain: b. Engineered: yes. 5'-d(p Gp Cp Gp Tp Cp Cp Ap (Ddx))-3'. Chain: c. Engineered: yes. 5'-d(p Gp Tp Cp Tp Ap Cp C)-3'. Chain: d.
Source: Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Gene: ogg1. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
2.05Å     R-factor:   0.239     R-free:   0.282
Authors: S.J.Chung,G.L.Verdine
Key ref:
S.J.Chung and G.L.Verdine (2004). Structures of end products resulting from lesion processing by a DNA glycosylase/lyase. Chem Biol, 11, 1643-1649. PubMed id: 15610848 DOI: 10.1016/j.chembiol.2004.09.014
27-Jun-02     Release date:   20-Apr-04    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O15527  (OGG1_HUMAN) -  N-glycosylase/DNA lyase
345 a.a.
314 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: 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.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   5 terms 
  Biological process     metabolic process   21 terms 
  Biochemical function     catalytic activity     12 terms  


DOI no: 10.1016/j.chembiol.2004.09.014 Chem Biol 11:1643-1649 (2004)
PubMed id: 15610848  
Structures of end products resulting from lesion processing by a DNA glycosylase/lyase.
S.J.Chung, G.L.Verdine.
DNA glycosylase/lyases initiate the repair of damaged nucleobases in the genome by catalyzing excision of aberrant nucleobases and nicking of the lesion-containing DNA strand. Nearly all of these proteins have the unusual property of remaining tightly bound in vitro to the end products of the reaction cascade. We have taken advantage of this property to crystallize and structurally characterize the end product resulting from complete DNA processing by a catalytically active mutant form of human 8-oxoguanine DNA glycosylase (D268E hOgg1). The resulting structure is consistent with the currently accepted catalytic mechanism for the protein. Unexpectedly, however, soaking of a nucleobase analog into the crystals results in religation of the DNA backbone in situ.
  Selected figure(s)  
Figure 1.
Figure 1. Proposed Mechanism for hOgg1-Catalyzed Excision of 8-Oxoguanine (oxoG) and Cleavage of the DNA Strand
Figure 2.
Figure 2. Active Site Structure of the End-Product Complex
  The above figures are reprinted by permission from Cell Press: Chem Biol (2004, 11, 1643-1649) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19674107 V.S.Sidorenko, A.P.Grollman, P.Jaruga, M.Dizdaroglu, and D.O.Zharkov (2009).
Substrate specificity and excision kinetics of natural polymorphic variants and phosphomimetic mutants of human 8-oxoguanine-DNA glycosylase.
  FEBS J, 276, 5149-5162.  
18205545 F.Altieri, C.Grillo, M.Maceroni, and S.Chichiarelli (2008).
DNA damage and repair: from molecular mechanisms to health implications.
  Antioxid Redox Signal, 10, 891-937.  
17090545 N.A.Kuznetsov, V.V.Koval, G.A.Nevinsky, K.T.Douglas, D.O.Zharkov, and O.S.Fedorova (2007).
Kinetic conformational analysis of human 8-oxoguanine-DNA glycosylase.
  J Biol Chem, 282, 1029-1038.  
17116430 T.K.Hazra, A.Das, S.Das, S.Choudhury, Y.W.Kow, and R.Roy (2007).
Oxidative DNA damage repair in mammalian cells: a new perspective.
  DNA Repair (Amst), 6, 470-480.  
17015827 A.Banerjee, and G.L.Verdine (2006).
A nucleobase lesion remodels the interaction of its normal neighbor in a DNA glycosylase complex.
  Proc Natl Acad Sci U S A, 103, 15020-15025.
PDB code: 2i5w
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