PDBsum entry 4d12

Oxidoreductase

PDB id: 4d12

Contents

Protein chain

301 a.a.

Ligands

MPD

URC

Waters ×598

PDB id:

4d12

Name:

Oxidoreductase

Title:

Crystal structure of cofactor-free urate oxidase anaerobically complexed with uric acid

Structure:

Uricase. Chain: a. Synonym: urate oxidase, urate oxidase. Engineered: yes

Source:

Aspergillus flavus. Organism_taxid: 5059. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.40Å R-factor: 0.119 R-free: 0.142

Authors:

S.Bui,R.A.Steiner

Key ref:

S.Bui et al. (2014). Direct evidence for a peroxide intermediate and a reactive enzyme-substrate-dioxygen configuration in a cofactor-free oxidase. Angew Chem Int Ed Engl, 53, 13710-13714. PubMed id: 25314114 DOI: 10.1002/anie.201405485

Date:

01-May-14 Release date: 29-Oct-14

Protein chain

Q00511  (URIC_ASPFL) -  Uricase from Aspergillus flavus

Seq: 302 a.a.

Struc: 301 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 = URC) corresponds exactly) = 5-hydroxyisourate + H2O2

• Cofactor: Copper

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

reference

DOI no: 10.1002/anie.201405485

Angew Chem Int Ed Engl 53:13710-13714 (2014)

PubMed id: 25314114

Direct evidence for a peroxide intermediate and a reactive enzyme-substrate-dioxygen configuration in a cofactor-free oxidase.

S.Bui, D.von Stetten, P.G.Jambrina, T.Prangé, N.Colloc'h, D.de Sanctis, A.Royant, E.Rosta, R.A.Steiner.

ABSTRACT

Cofactor-free oxidases and oxygenases promote and control the reactivity of O2 with limited chemical tools at their disposal. Their mechanism of action is not completely understood and structural information is not available for any of the reaction intermediates. Near-atomic resolution crystallography supported by in crystallo Raman spectroscopy and QM/MM calculations showed unambiguously that the archetypical cofactor-free uricase catalyzes uric acid degradation via a C5(S)-(hydro)peroxide intermediate. Low X-ray doses break specifically the intermediate C5OO(H) bond at 100 K, thus releasing O2 in situ, which is trapped above the substrate radical. The dose-dependent rate of bond rupture followed by combined crystallographic and Raman analysis indicates that ionizing radiation kick-starts both peroxide decomposition and its regeneration. Peroxidation can be explained by a mechanism in which the substrate radical recombines with superoxide transiently produced in the active site.