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PDBsum entry 3l9g

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protein ligands metals links
Oxidoreductase PDB id
3l9g
Jmol
Contents
Protein chain
296 a.a. *
Ligands
URC
MRD
Metals
_NA
_CL
Waters ×248
* Residue conservation analysis
PDB id:
3l9g
Name: Oxidoreductase
Title: Urate oxidase complexed with uric acid and chloride
Structure: Uricase. Chain: a. Fragment: unp residues 2-296. Synonym: urate oxidase. Engineered: yes
Source: Aspergillus flavus. Organism_taxid: 5059. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932
Resolution:
1.75Å     R-factor:   0.179     R-free:   0.208
Authors: T.Prange,N.Colloc'H,L.Gabison
Key ref: L.Gabison et al. (2010). Near-atomic resolution structures of urate oxidase complexed with its substrate and analogues: the protonation state of the ligand. Acta Crystallogr D Biol Crystallogr, 66, 714-724. PubMed id: 20516624
Date:
05-Jan-10     Release date:   02-Jun-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q00511  (URIC_ASPFL) -  Uricase
Seq:
Struc:
302 a.a.
295 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.7.3.3  - Factor independent urate hydroxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
AMP Catabolism
      Reaction: Urate + O2 + H2O = 5-hydroxyisourate + H2O2
Urate
Bound ligand (Het Group name = URC)
corresponds exactly
+ O(2)
+ H(2)O
= 5-hydroxyisourate
+ H(2)O(2)
      Cofactor: Copper
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     peroxisome   1 term 
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     2 terms  

 

 
    reference    
 
 
Acta Crystallogr D Biol Crystallogr 66:714-724 (2010)
PubMed id: 20516624  
 
 
Near-atomic resolution structures of urate oxidase complexed with its substrate and analogues: the protonation state of the ligand.
L.Gabison, M.Chiadmi, M.El Hajji, B.Castro, N.Colloc'h, T.Prangé.
 
  ABSTRACT  
 
Urate oxidase (uricase; EC 1.7.3.3; UOX) from Aspergillus flavus catalyzes the oxidation of uric acid in the presence of molecular oxygen to 5-hydroxyisourate in the degradation cascade of purines; intriguingly, catalysis proceeds using neither a metal ion (Fe, Cu etc.) nor a redox cofactor. UOX is a tetrameric enzyme with four active sites located at the interface of two subunits; its structure was refined at atomic resolution (1 A) using new crystal data in the presence of xanthine and at near-atomic resolution (1.3-1.7 A) in complexes with the natural substrate (urate) and two inhibitors: 8-nitroxanthine and 8-thiouric acid. Three new features of the structural and mechanistic behaviour of the enzyme were addressed. Firstly, the high resolution of the UOX-xanthine structure allowed the solution of an old structural problem at a contact zone within the tetramer; secondly, the protonation state of the substrate was determined from both a halochromic inhibitor complex (UOX-8-nitroxanthine) and from the H-atom distribution in the active site, using the structures of the UOX-xanthine and the UOX-uric acid complexes; and thirdly, it was possible to extend the general base system, characterized by the conserved catalytic triad Thr-Lys-His, to a large water network that is able to buffer and shuttle protons back and forth between the substrate and the peroxo hole along the reaction pathway.