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PDBsum entry 3bk8

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protein ligands metals links
Oxidoreductase PDB id
3bk8
Jmol
Contents
Protein chain
295 a.a. *
Ligands
AZA
Metals
_NA
Waters ×280
* Residue conservation analysis
PDB id:
3bk8
Name: Oxidoreductase
Title: Urate oxidase aza-xanthine complex in cyanide
Structure: Uricase. Chain: a. Synonym: urate oxidase. Engineered: yes
Source: Aspergillus flavus. Organism_taxid: 5059. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932
Resolution:
1.60Å     R-factor:   0.203     R-free:   0.230
Authors: L.Gabison,T.Prange,N.Colloc'H,M.El Hajji,B.Castro,M.Chiadmi
Key ref: L.Gabison et al. (2008). Structural analysis of urate oxidase in complex with its natural substrate inhibited by cyanide: mechanistic implications. BMC Struct Biol, 8, 32-32. PubMed id: 18638417
Date:
06-Dec-07     Release date:   12-Aug-08    
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 = AZA)
matches with 76.00% similarity
+ 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    
 
 
BMC Struct Biol 8:32-32 (2008)
PubMed id: 18638417  
 
 
Structural analysis of urate oxidase in complex with its natural substrate inhibited by cyanide: mechanistic implications.
L.Gabison, T.Prangé, N.Colloc'h, M.El Hajji, B.Castro, M.Chiadmi.
 
  ABSTRACT  
 
BACKGROUND: Urate oxidase (EC 1.7.3.3 or UOX) catalyzes the conversion of uric acid and gaseous molecular oxygen to 5-hydroxyisourate and hydrogen peroxide, in the absence of cofactor or particular metal cation. The functional enzyme is a homo-tetramer with four active sites located at dimeric interfaces. RESULTS: The catalytic mechanism was investigated through a ternary complex formed between the enzyme, uric acid, and cyanide that stabilizes an intermediate state of the reaction. When uric acid is replaced by a competitive inhibitor, no complex with cyanide is formed. CONCLUSION: The X-ray structure of this compulsory ternary complex led to a number of mechanistic evidences that support a sequential mechanism in which the two reagents, dioxygen and a water molecule, process through a common site located 3.3 A above the mean plane of the ligand. This site is built by the side chains of Asn 254, and Thr 57, two conserved residues belonging to two different subunits of the homo-tetramer. The absence of a ternary complex between the enzyme, a competitive inhibitor, and cyanide suggests that cyanide inhibits the hydroxylation step of the reaction, after the initial formation of a hydroperoxyde type intermediate.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21491497 L.Gabison, C.Chopard, N.Colloc'h, F.Peyrot, B.Castro, M.E.Hajji, M.Altarsha, G.Monard, M.Chiadmi, and T.Prangé (2011).
X-ray, ESR, and quantum mechanics studies unravel a spin well in the cofactor-less urate oxidase.
  Proteins, 79, 1964-1976.
PDB code: 3obp
20483346 E.Girard, S.Marchal, J.Perez, S.Finet, R.Kahn, R.Fourme, G.Marassio, A.C.Dhaussy, T.Prangé, M.Giffard, F.Dulin, F.Bonneté, R.Lange, J.H.Abraini, M.Mezouar, and N.Colloc'h (2010).
Structure-function perturbation and dissociation of tetrameric urate oxidase by high hydrostatic pressure.
  Biophys J, 98, 2365-2373.
PDB code: 3f2m
20157809 S.Fetzner, and R.A.Steiner (2010).
Cofactor-independent oxidases and oxygenases.
  Appl Microbiol Biotechnol, 86, 791-804.  
19586953 E.Oksanen, M.P.Blakeley, F.Bonneté, M.T.Dauvergne, F.Dauvergne, and M.Budayova-Spano (2009).
Large crystal growth by thermal control allows combined X-ray and neutron crystallographic studies to elucidate the protonation states in Aspergillus flavus urate oxidase.
  J R Soc Interface, 6, S599-S610.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.