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PDBsum entry 2opf

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protein dna_rna ligands metals links
Hydrolase/DNA PDB id
2opf
Jmol
Contents
Protein chain
256 a.a. *
DNA/RNA
Ligands
SO4
GOL ×5
Metals
_ZN
Waters ×243
* Residue conservation analysis
PDB id:
2opf
Name: Hydrolase/DNA
Title: Crystal structure of the DNA repair enzyme endonuclease-viii from e. Coli (r252a) in complex with ap-site containing dna
Structure: Endonuclease viii. Chain: a. Synonym: DNA glycosylase/ap lyase nei, DNA-apurinic or apyr site, lyase nei. Engineered: yes. Mutation: yes. 5'-d( Gp Gp Cp Tp Tp Cp Ap Tp Cp Cp Tp G)-3'. Chain: b. Engineered: yes.
Source: Escherichia coli. Organism_taxid: 562. Gene: nei. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes
Resolution:
1.85Å     R-factor:   0.240     R-free:   0.267
Authors: G.Golan,D.O.Zharov,A.P.Grollman,G.Shoham
Key ref: G.Golan et al. Active site plasticity of endonuclease VIII: conformational changes compensating for different substrates and mutations of critical residues. To be published, .
Date:
29-Jan-07     Release date:   26-Feb-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P50465  (END8_ECOLI) -  Endonuclease 8
Seq:
Struc:
263 a.a.
256 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.4.2.99.18  - 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   7 terms 
  Biochemical function     catalytic activity     13 terms