1WRR

Urate oxidase from aspergillus flavus complexed with 5-amino 6-nitro uracil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Urate oxidase from Aspergillus flavus: new crystal-packing contacts in relation to the content of the active site.

Retailleau, P.Colloc'h, N.Vivares, D.Bonnete, F.Castro, B.El Hajji, M.Prange, T.

(2005) Acta Crystallogr.,Sect.D 61: 218-229

  • DOI: 10.1107/S0907444904031531
  • Primary Citation of Related Structures:  

  • PubMed 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 enzy ...

    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.


    Related Citations: 
    • Crystal structure of the protein drug urate oxidase-inhibitor complex at 2.05 A resolution
      Colloc'h, N.,El Hajji, M.,Bachet, B.,L'Hermite, G.,Schiltz, M.,Castro, B.,Mornon, J.P.
      (1997) Nat.Struct.Mol.Biol. 4: 947


    Organizational Affiliation

    LURE, Centre Universitaire Paris-Sud, B√Ętiment 209D, BP 34, 91898 Orsay CEDEX, France. pascal.retaileau@icsn.cnrs-gif.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uricase
A
301Aspergillus flavusMutation(s): 0 
Gene Names: uaZ (uox)
EC: 1.7.3.3
Find proteins for Q00511 (Aspergillus flavus)
Go to UniProtKB:  Q00511
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNC
Query on UNC

Download SDF File 
Download CCD File 
A
5-AMINO-6-NITROPYRIMIDINE-2,4(1H,3H)-DIONE
5-AMINO 6-NITRO URACIL
C4 H4 N4 O4
CLOSWQFGCBFNCK-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SAC
Query on SAC
A
L-PEPTIDE LINKINGC5 H9 N O4SER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.168 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 80.385α = 90.00
b = 96.469β = 90.00
c = 106.131γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2018-02-28
    Type: Structure summary