PDBsum entry 1q3c

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Hydrolase PDB id
Jmol PyMol
Protein chain
250 a.a. *
GOL ×3
_MG ×2
Waters ×75
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of the DNA repair enzyme endonuclease-viii from e. Coli: the e2a mutant at 2.3 resolution.
Structure: Endonuclease viii. Chain: a. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: nei. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
2.30Å     R-factor:   0.245     R-free:   0.304
Authors: G.Golan,D.O.Zharkov,H.Feinberg,A.S.Fernandes,E.I.Zaika,J.H.K A.P.Grollman,G.Shoham
Key ref: G.Golan et al. (2005). Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility. Nucleic Acids Res, 33, 5006-5016. PubMed id: 16145054
29-Jul-03     Release date:   03-Aug-04    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P50465  (END8_ECOLI) -  Endonuclease 8
263 a.a.
250 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 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!
  Biological process     metabolic process   6 terms 
  Biochemical function     catalytic activity     11 terms  


Nucleic Acids Res 33:5006-5016 (2005)
PubMed id: 16145054  
Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility.
G.Golan, D.O.Zharkov, H.Feinberg, A.S.Fernandes, E.I.Zaika, J.H.Kycia, A.P.Grollman, G.Shoham.
Escherichia coli endonuclease VIII (Nei) excises oxidized pyrimidines from DNA. It shares significant sequence homology and similar mechanism with Fpg, a bacterial 8-oxoguanine glycosylase. The structure of a covalent Nei-DNA complex has been recently determined, revealing critical amino acid residues which are important for DNA binding and catalysis. Several Fpg structures have also been reported; however, analysis of structural dynamics of Fpg/Nei family proteins has been hindered by the lack of structures of uncomplexed and DNA-bound enzymes from the same source. We report a 2.8 A resolution structure of free wild-type Nei and two structures of its inactive mutants, Nei-E2A (2.3 A) and Nei-R252A (2.05 A). All three structures are virtually identical, demonstrating that the mutations did not affect the overall conformation of the protein in its free state. The structures show a significant conformational change compared with the Nei structure in its complex with DNA, reflecting a approximately 50 degrees rotation of the two main domains of the enzyme. Such interdomain flexibility has not been reported previously for any DNA glycosylase and may present the first evidence for a global DNA-induced conformational change in this class of enzymes. Several local but functionally relevant structural changes are also evident in other parts of the enzyme.
  Selected figure(s)  
Figure 2.
Solvent-accessible surface of free Nei, colored according to electrostatic potential (positive in blue, negative in red and neutral in gray), demonstrating the highly positive DNA-binding cleft of the enzyme (left center). Locations of three important residues involved in DNA binding are indicated by arrows.
Figure 5.
The zinc finger motif of Nei. An electron density map is shown around the bound zinc atom [`omit' map at contour levels of 5 [220]{sigma} (blue), and 17 {sigma} (green)]. The four Cys residues (with typical Zn-S bond lengths of 2.28-2.38 ) are shown in a ball-and-stick representation and the two anti-parallel -strands are shown in a ribbon diagram (beige). Superimposed on this region is the corresponding region of the Nei-DNA complex (red), demonstrating a movement of the tip of the zinc finger between the free and the DNA-bound forms of the enzyme.
  The above figures are reprinted from an Open Access publication published by Oxford University Press: Nucleic Acids Res (2005, 33, 5006-5016) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
17002303 K.Y.Kropachev, D.O.Zharkov, and A.P.Grollman (2006).
Catalytic mechanism of Escherichia coli endonuclease VIII: roles of the intercalation loop and the zinc finger.
  Biochemistry, 45, 12039-12049.  
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