3PK4

Urate oxidase under 3.2 MPa / 32 bars pressure of xenon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Pressure-response analysis of anesthetic gases xenon and nitrous oxide on urate oxidase: a crystallographic study.

Marassio, G.Prange, T.David, H.N.Sopkova-de Oliveira Santos, J.Gabison, L.Delcroix, N.Abraini, J.H.Colloc'h, N.

(2011) FASEB J 25: 2266-2275

  • DOI: https://doi.org/10.1096/fj.11-183046
  • Primary Citation of Related Structures:  
    3PJK, 3PK3, 3PK4, 3PK5, 3PK6, 3PK8, 3PKF, 3PKG, 3PKH, 3PKK, 3PKL, 3PKS, 3PKT, 3PKU, 3PLE, 3PLG, 3PLH, 3PLI, 3PLJ, 3PLM

  • PubMed Abstract: 

    The remarkably safe anesthetics xenon (Xe) and, to lesser extent, nitrous oxide (N(2)O) possess neuroprotective properties in preclinical studies. To investigate the mechanisms of pharmacological action of these gases, which are still poorly known, we performed both crystallography under a large range of gas pressure and biochemical studies on urate oxidase, a prototype of globular gas-binding proteins whose activity is modulated by inert gases. We show that Xe and N(2)O bind to, compete for, and expand the volume of a hydrophobic cavity located just behind the active site of urate oxidase and further inhibit urate oxidase enzymatic activity. By demonstrating a significant relationship between the binding and biochemical effects of Xe and N(2)O, given alone or in combination, these data from structure to function highlight the mechanisms by which chemically and metabolically inert gases can alter protein function and produce their pharmacological effects. Interestingly, the effects of a Xe:N(2)O equimolar mixture were found to be equivalent to those of Xe alone, thereby suggesting that gas mixtures containing Xe and N(2)O could be an alternative and efficient neuroprotective strategy to Xe alone, whose widespread clinical use is limited due to the cost of production and availability of this gas.


  • Organizational Affiliation

    Equipe de Recherche Technologique Interne (ERTi) 1083, Centre National de la Recherche Scientifique (CNRS), Centre Cyceron, Caen, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uricase302Aspergillus flavusMutation(s): 1 
Gene Names: uaZuox
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
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.405α = 90
b = 96.311β = 90
c = 105.593γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-27
    Changes: Structure summary