2FXL | pdb_00002fxl

Urate oxidase from aspergillus flavus complexed with allantoin

• PDB DOI: https://doi.org/10.2210/pdb2FXL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aspergillus flavus
• Expression System: Saccharomyces cerevisiae
• Mutation(s): Yes 


• Deposited: 2006-02-06 Released: 2006-05-23 
• Deposition Author(s): Gabison, L., Chiadmi, M., Colloc'h, N., Prange, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Work: 
  0.183 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Recapture of [S]-allantoin, the product of the two-step degradation of uric acid, by urate oxidase.

Gabison, L., Chiadmi, M., Colloc'h, N., Castro, B., El Hajji, M., Prange, T.

(2006) FEBS Lett 580: 2087-2091

• PubMed: 16545381 
• DOI: https://doi.org/10.1016/j.febslet.2006.03.007
• Primary Citation Related Structures: 
  2FXL


• PubMed Abstract: 
  

  Urate oxidase from Aspergillus flavus catalyzes the degradation of uric acid to [S]-allantoin through 5-hydroxyisourate as a metastable intermediate. The second degradation step is thought either catalyzed by another specific enzyme, or spontaneous. The structure of the enzyme was known at high resolution by X-ray diffraction of I222 crystals complexed with a purine-type inhibitor (8-azaxanthin). Analyzing the X-ray structure of urate oxidase treated with an excess of urate, the natural substrate, shows unexpectedly that the active site recaptures [S]-allantoin from the racemic end product of a second degradation step.

---

Organizational Affiliation: 
• Laboratoire de cristallographie et RMN biologiques (UMR 8015 CNRS), Faculté de Pharmacie, Université Paris V, 4 avenue de l'Observatoire, 75270 Paris Cedex 06, France.

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: 2,565 
• Modeled 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  Gene Names: uaZ, uox 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
2AL	B [auth A]	1-(2,5-DIOXO-2,5-DIHYDRO-1H-IMIDAZOL-4-YL)UREA C4 H4 N4 O3 MFAONEQLPARJAO-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: 1.76 Å
• R-Value Work:  0.183 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.364	α = 90
b = 96.086	β = 90
c = 105.368	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELXL	refinement
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-23 
Deposition Author(s): Gabison, L., Chiadmi, M., Colloc'h, N., Prange, T.

Revision History  

• Version 1.0: 2006-05-23
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2018-02-28
  Changes: Structure summary
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description