PDBsum entry 1ws3

Oxidoreductase

PDB id: 1ws3

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

Protein chains

Q00511  (URIC_ASPFL) -  Uricase from Aspergillus flavus

Seq: 302 a.a.

Struc: 296 a.a.*

* 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.
• Pathway: AMP Catabolism
• Reaction: urate + O2 + H2O = 5-hydroxyisourate + H2O2

urate + O2 + H2O (Bound ligand (Het Group name = URA) matches with 66.67% similarity) = 5-hydroxyisourate + H2O2

• Cofactor: Copper

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

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.