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PDBsum entry 1ws3

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1ws3
Jmol
Contents
Protein chains
296 a.a. *
Ligands
URA ×4
* Residue conservation analysis
PDB id:
1ws3
Name: Oxidoreductase
Title: Urate oxidase from aspergillus flavus complexed with uracil
Structure: Uricase. Chain: a, b, c, d. Synonym: urate oxidase. Engineered: yes
Source: Aspergillus flavus. Organism_taxid: 5059. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932
Biol. unit: Tetramer (from PQS)
Resolution:
3.20Å     R-factor:   0.146     R-free:   0.200
Authors: P.Retailleau,N.Colloc'H,D.Vivares,F.Bonnete,B.Castro,M.El Hajji,T.Prange
Key ref:
P.Retailleau et al. (2005). Urate oxidase from Aspergillus flavus: new crystal-packing contacts in relation to the content of the active site. Acta Crystallogr D Biol Crystallogr, 61, 218-229. PubMed id: 15735331 DOI: 10.1107/S0907444904031531
Date:
29-Oct-04     Release date:   22-Mar-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q00511  (URIC_ASPFL) -  Uricase
Seq:
Struc:
302 a.a.
296 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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 = URA)
matches with 66.00% 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    
 
 
DOI no: 10.1107/S0907444904031531 Acta Crystallogr D Biol Crystallogr 61:218-229 (2005)
PubMed id: 15735331  
 
 
Urate oxidase from Aspergillus flavus: new crystal-packing contacts in relation to the content of the active site.
P.Retailleau, N.Colloc'h, D.Vivarès, F.Bonneté, B.Castro, M.El Hajji, T.Prangé.
 
  ABSTRACT  
 
Urate oxidase from Aspergillus flavus (uricase or Uox; EC 1.7.3.3) is a 135 kDa homotetramer with a subunit consisting of 301 amino acids. It catalyses the first step of the degradation of uric acid into allantoin. The structure of the extracted enzyme complexed with a purine-type inhibitor (8-azaxanthin) had been solved from high-resolution X-ray diffraction of I222 crystals. Expression of the recombinant enzyme in Saccharomyces cerevisiae followed by a new purification procedure allowed the crystallization of both unliganded and liganded enzymes utilizing the same conditions but in various crystal forms. Here, four different crystal forms of Uox are analyzed. The diversity of the Uox crystal forms appears to depend strongly on the chemicals used as inhibitors. In the presence of uracil and 5,6-diaminouracil crystals usually belong to the trigonal space group P3(1)21, the asymmetric unit (AU) of which contains one tetramer of Uox (four subunits). Chemical oxidation of 5,6-diaminouracil within the protein may occur, leading to the canonical (I222) packing with one subunit per AU. Coexistence of two crystal forms, P2(1) with two tetramers per AU and I222, was found in the same crystallization drop containing another inhibitor, guanine. Finally, a fourth form, P2(1)2(1)2 with one tetramer per AU, resulted fortuitously in the presence of cymelarsan, an additive. Of all the reported forms, the I222 crystal forms present by far the best X-ray diffraction resolution (approximately 1.6 angstroms resolution compared with 2.3-3.2 angstroms for the other forms). The various structures and contacts in all crystalline lattices are compared. The backbones are essentially conserved except for the region near the active site. Its location at the dimer interface is thus likely to be at the origin of the crystal contact changes as a response to the various bound inhibitors.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 View of the active site: the omit map is contoured at the 1.5 [118][sigma] level around the 5-amino-6-nitrouracil with the model superimposed. Graphics were created using MOLSCRIPT (Kraulis, 1991[119] [Kraulis, P. E. (1991). J. Appl. Cryst. 24, 946-950.]-[120][bluearr.gif] ) and rendered using RASTER3D (Merritt & Murphy, 1994[121] [Merritt, E. A. & Murphy, M. E. P. (1994). Acta Cryst. D50, 869-873.]-[122][bluearr.gif] ).
Figure 2.
Figure 2 The reaction pathway from uric acid to 5-hydroxyisourate (middle) and the analogues used. Note that uracil (and derivatives) standard numberings differ compared with uric acid derivatives. *, Kahn & Tipton (1997[159] [Kahn, K. & Tipton, P. A. (1997). Biochemistry, 36, 4731-4738.]-[160][bluearr.gif] ); **, Pfleiderer (1974[161] [Pfleiderer, W. (1974). Liebigs Ann. Chem. 12, 2030-2045.]-[162][bluearr.gif] ).
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 218-229) copyright 2005.  
  Figures were selected by an automated process.  

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
20606256 G.Pompidor, O.Maury, J.Vicat, and R.Kahn (2010).
A dipicolinate lanthanide complex for solving protein structures using anomalous diffraction.
  Acta Crystallogr D Biol Crystallogr, 66, 762-769.
PDB codes: 2pe7 2pes 3lgr
20445229 I.Collings, Y.Watier, M.Giffard, S.Dagogo, R.Kahn, F.Bonneté, J.P.Wright, A.N.Fitch, and I.Margiolaki (2010).
Polymorphism of microcrystalline urate oxidase from Aspergillus flavus.
  Acta Crystallogr D Biol Crystallogr, 66, 539-548.  
20516624 L.Gabison, M.Chiadmi, M.El Hajji, B.Castro, N.Colloc'h, and T.Prangé (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.
PDB codes: 3l8w 3l9g 3lbg 3ld4
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.  
18638417 L.Gabison, T.Prangé, N.Colloc'h, M.El Hajji, B.Castro, and M.Chiadmi (2008).
Structural analysis of urate oxidase in complex with its natural substrate inhibited by cyanide: mechanistic implications.
  BMC Struct Biol, 8, 32.
PDB codes: 3bjp 3bk8
16782815 D.K.Jung, Y.Lee, S.G.Park, B.C.Park, G.H.Kim, and S.Rhee (2006).
Structural and functional analysis of PucM, a hydrolase in the ureide pathway and a member of the transthyretin-related protein family.
  Proc Natl Acad Sci U S A, 103, 9790-9795.
PDB codes: 2h0e 2h0f 2h0j
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.