3CKU

Urate oxidase from aspergillus flavus complexed with its inhibitor 8-azaxanthin and chloride


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Oxygen pressurized X-ray crystallography: probing the dioxygen binding site in cofactorless urate oxidase and implications for its catalytic mechanism.

Colloc'h, N.Gabison, L.Monard, G.Altarsha, M.Chiadmi, M.Marassio, G.Sopkova-de Oliveira Santos, J.El Hajji, M.Castro, B.Abraini, J.H.Prange, T.

(2008) Biophys.J. 95: 2415-2422

  • DOI: 10.1529/biophysj.107.122184
  • Primary Citation of Related Structures:  
  • Also Cited By: 3L8W, 3L9G

  • PubMed Abstract: 
  • The localization of dioxygen sites in oxygen-binding proteins is a nontrivial experimental task and is often suggested through indirect methods such as using xenon or halide anions as oxygen probes. In this study, a straightforward method based on x- ...

    The localization of dioxygen sites in oxygen-binding proteins is a nontrivial experimental task and is often suggested through indirect methods such as using xenon or halide anions as oxygen probes. In this study, a straightforward method based on x-ray crystallography under high pressure of pure oxygen has been developed. An application is given on urate oxidase (UOX), a cofactorless enzyme that catalyzes the oxidation of uric acid to 5-hydroxyisourate in the presence of dioxygen. UOX crystals in complex with a competitive inhibitor of its natural substrate are submitted to an increasing pressure of 1.0, 2.5, or 4.0 MPa of gaseous oxygen. The results clearly show that dioxygen binds within the active site at a location where a water molecule is usually observed but does not bind in the already characterized specific hydrophobic pocket of xenon. Moreover, crystallizing UOX in the presence of a large excess of chloride (NaCl) shows that one chloride ion goes at the same location as the oxygen. The dioxygen hydrophilic environment (an asparagine, a histidine, and a threonine residues), its absence within the xenon binding site, and its location identical to a water molecule or a chloride ion suggest that the dioxygen site is mainly polar. The implication of the dioxygen location on the mechanism is discussed with respect to the experimentally suggested transient intermediates during the reaction cascade.


    Related Citations: 
    • Complexed and ligand-free high-resolution structures of urate oxidase (Uox) from Aspergillus flavus: a reassignment of the active-site binding mode.
      Retailleau, P.,Colloc'h, N.,Vivares, D.,Bonnete, F.,Castro, B.,El-Hajji, M.,Mornon, J.P.,Monard, G.,Prange, T.
      (2004) Acta Crystallogr.,Sect.D 60: 453
    • Protein crystallography under xenon and nitrous oxide pressure: comparison with in vivo pharmacology studies and implications for the mechanism of inhaled anesthetic action.
      Colloc'h, N.,Sopkova-de Oliveira Santos, J.,Retailleau, P.,Vivares, D.,Bonnete, F.,Langlois d'Estainto, B.,Gallois, B.,Brisson, A.,Risso, J.J.,Lemaire, M.,Prange, T.,Abraini, J.H.
      (2007) Biophys.J. 92: 217
    • 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.,Prange, T.,Castro, B.,Mornon, J.P.
      (1997) Nat.Struct.Mol.Biol. 4: 947


    Organizational Affiliation

    CI-NAPS, UMR 6232-UCBN-CNRS-CEA, Centre Cyceron, 14074 Caen cedex, France. colloch@cyceron.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uricase
A
302Aspergillus 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
AZA
Query on AZA

Download SDF File 
Download CCD File 
A
8-AZAXANTHINE
C4 H3 N5 O2
KVGVQTOQSNJTJI-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.193 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 78.994α = 90.00
b = 94.979β = 90.00
c = 104.381γ = 90.00
Software Package:
Software NamePurpose
DNAdata collection
MOSFLMdata reduction
SHELXL-97refinement
SCALAdata scaling
SHELXmodel building
FFTphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance