Crystal structure of cofactor-free urate oxidase in complex with its 5-peroxoisourate intermediate (X-ray dose, 1.75 MGy)

Experimental Data Snapshot

  • Resolution: 1.35 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.106 
  • R-Value Observed: 0.108 

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

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

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

  • DOI: https://doi.org/10.1002/anie.201405485
  • Primary Citation of Related Structures:  
    4CW0, 4CW2, 4CW3, 4CW6, 4D12, 4D13, 4D17, 4D19

  • PubMed 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.

  • Organizational Affiliation

    Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL (UK).

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
URICASE302Aspergillus flavusMutation(s): 0 
Find proteins for Q00511 (Aspergillus flavus)
Explore Q00511 
Go to UniProtKB:  Q00511
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00511
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.35 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.106 
  • R-Value Observed: 0.108 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.94α = 90
b = 95.13β = 90
c = 104.11γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-29
    Type: Initial release
  • Version 1.1: 2014-12-17
    Changes: Database references
  • Version 1.2: 2017-12-13
    Changes: Database references
  • Version 1.3: 2018-02-21
    Changes: Database references
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other