1R4U

URATE OXIDASE FROM ASPERGILLUS FLAVUS COMPLEXED WITH ITS INHIBITOR OXONIC ACID

• PDB DOI: https://doi.org/10.2210/pdb1R4U/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aspergillus flavus
• Mutation(s): Yes 


• Deposited: 2003-10-08 Released: 2004-03-02 
• Deposition Author(s): Retailleau, P., Colloc'h, N., Prange, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.182 
• R-Value Work: 0.157 

Starting Model: experimental

Literature

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 D Biol Crystallogr 60: 453-462

• PubMed: 14993669 
• DOI: https://doi.org/10.1107/S0907444903029718
• Primary Citation of Related Structures:  
  1R4S, 1R4U, 1R51, 1R56


• PubMed Abstract: 
  

  High-resolution X-ray structures of the complexes of Aspergillus flavus urate oxidase (Uox) with three inhibitors, 8-azaxanthin (AZA), 9-methyl uric acid (MUA) and oxonic acid (OXC), were determined in an orthorhombic space group (I222). In addition, the ligand-free enzyme was also crystallized in a monoclinic form (P2(1)) and its structure determined. Higher accuracy in the three new enzyme-inhibitor complex structures (Uox-AZA, Uox-MUA and Uox-OXC) with respect to the previously determined structure of Uox-AZA (PDB code 1uox) leads to a reversed position of the inhibitor in the active site of the enzyme. The corrected anchoring of the substrate (uric acid) allows an improvement in the understanding of the enzymatic mechanism of urate oxidase.

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Organizational Affiliation: 

LURE, Centre Universitaire Paris-Sud, Bâtiment 209D, BP 34, 91898 Orsay CEDEX, France. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 34.36 kDa 
• Atom Count: 2,600 
• Modelled Residue Count: 295 
• Deposited Residue Count: 301 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uricase	A	301	Aspergillus flavus	Mutation(s): 1  EC: 1.7.3.3
UniProt
Find proteins for Q00511 (Aspergillus flavus) Explore Q00511  Go to UniProtKB:  Q00511

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OXC	B [auth A]	OXONIC ACID C4 H5 N3 O4 IRFZLMWJJPULRF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SAC	A	L-PEPTIDE LINKING	C5 H9 N O4		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.182 
• R-Value Work: 0.157 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.702	α = 90
b = 96.075	β = 90
c = 105.589	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
BUSTER-TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-02 
Deposition Author(s): Retailleau, P., Colloc'h, N., Prange, T.

Revision History  

• Version 1.0: 2004-03-02
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2018-02-28
  Changes: Database references, Structure summary
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description