PDBsum entry 3ld4

Oxidoreductase

PDB id: 3ld4

Contents

Protein chain

296 a.a. *

Ligands

8NX

EDO

Metals

_NA

Waters ×265

* Residue conservation analysis

PDB id:

3ld4

Name:

Oxidoreductase

Title:

Urate oxidase complexed with 8-nitro xanthine

Structure:

Uricase. Chain: a. Fragment: unp residues 2-296. Synonym: urate oxidase. Engineered: yes

Source:

Aspergillus flavus. Organism_taxid: 5059. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932

Resolution:

1.35Å R-factor: 0.192 R-free: 0.225

Authors:

T.Prange,N.Colloc'H,L.Gabison

Key ref:

L.Gabison et al. (2010). Near-atomic resolution structures of urate oxidase complexed with its substrate and analogues: the protonation state of the ligand. Acta Crystallogr D Biol Crystallogr, 66, 714-724. PubMed id: 20516624

Date:

12-Jan-10 Release date: 02-Jun-10

Protein chain

Q00511  (URIC_ASPFL) -  Uricase from Aspergillus flavus

Seq: 302 a.a.

Struc: 295 a.a.

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 = 8NX) matches with 73.33% similarity) = 5-hydroxyisourate + H2O2

• Cofactor: Copper

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

reference

Acta Crystallogr D Biol Crystallogr 66:714-724 (2010)

PubMed id: 20516624

Near-atomic resolution structures of urate oxidase complexed with its substrate and analogues: the protonation state of the ligand.

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

ABSTRACT

Urate oxidase (uricase; EC 1.7.3.3; UOX) from Aspergillus flavus catalyzes the oxidation of uric acid in the presence of molecular oxygen to 5-hydroxyisourate in the degradation cascade of purines; intriguingly, catalysis proceeds using neither a metal ion (Fe, Cu etc.) nor a redox cofactor. UOX is a tetrameric enzyme with four active sites located at the interface of two subunits; its structure was refined at atomic resolution (1 A) using new crystal data in the presence of xanthine and at near-atomic resolution (1.3-1.7 A) in complexes with the natural substrate (urate) and two inhibitors: 8-nitroxanthine and 8-thiouric acid. Three new features of the structural and mechanistic behaviour of the enzyme were addressed. Firstly, the high resolution of the UOX-xanthine structure allowed the solution of an old structural problem at a contact zone within the tetramer; secondly, the protonation state of the substrate was determined from both a halochromic inhibitor complex (UOX-8-nitroxanthine) and from the H-atom distribution in the active site, using the structures of the UOX-xanthine and the UOX-uric acid complexes; and thirdly, it was possible to extend the general base system, characterized by the conserved catalytic triad Thr-Lys-His, to a large water network that is able to buffer and shuttle protons back and forth between the substrate and the peroxo hole along the reaction pathway.