4CW6

Crystal structure of cofactor-free urate oxidase in complex with the 5-peroxo derivative of 9-metyl uric acid (X-ray dose, 92 kGy)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.132 
  • R-Value Work: 0.112 
  • R-Value Observed: 0.113 

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Literature

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: 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 ...

    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).



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
URICASEA301Aspergillus flavusMutation(s): 0 
Gene Names: uaZ, uox
EC: 1.7.3.3
UniProt
Find proteins for Q00511 (Aspergillus flavus)
Explore Q00511 
Go to UniProtKB:  Q00511
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00511
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XDS
Query on XDS
Download Ideal Coordinates CCD File 
B [auth A](5S)-5-(dioxidanyl)-9-methyl-7H-purine-2,6,8-trione
C6 H6 N4 O5
JQXTWGOGXIASQD-LURJTMIESA-N		 Ligand Interaction
MUA
Query on MUA
Download Ideal Coordinates CCD File 
E [auth A]9-METHYL URIC ACID
C6 H6 N4 O3
XJEJWDFDVPDMAS-UHFFFAOYSA-N		 Ligand Interaction
MPD
Query on MPD
Download Ideal Coordinates CCD File 
C [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N		 Ligand Interaction
OXY
Query on OXY
Download Ideal Coordinates CCD File 
D [auth A]OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SAC
Query on SAC		A L-PEPTIDE LINKINGC5 H9 N O4SER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.132 
  • R-Value Work: 0.112 
  • R-Value Observed: 0.113 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.501α = 90
b = 95.138β = 90
c = 104.354γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
pointlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2014-04-01 
  • Released Date: 2014-10-29 
    • Deposition Author(s): Bui, S., Steiner, R.A.

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: 2017-06-21
    Changes: Refinement description
  • Version 1.3: 2017-12-20
    Changes: Database references
  • Version 1.4: 2018-02-21
    Changes: Database references