3F2M

Urate oxidase complexed with 8-azaxanthine at 150 MPa

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structure-function perturbation and dissociation of tetrameric urate oxidase by high hydrostatic pressure.

Girard, E., Marchal, S., Perez, J., Finet, S., Kahn, R., Fourme, R., Marassio, G., Dhaussy, A.C., Prange, T., Giffard, M., Dulin, F., Bonnete, F., Lange, R., Abraini, J.H., Mezouar, M., Colloc'h, N.

(2010) Biophys.J. 98: 2365-2373

  • DOI: 10.1016/j.bpj.2010.01.058

  • PubMed Abstract: 

    • Structure-function relationships in the tetrameric enzyme urate oxidase were investigated using pressure perturbation. As the active sites are located at the interfaces between monomers, enzyme activity is directly related to the integrity of the tet ...

    Structure-function relationships in the tetrameric enzyme urate oxidase were investigated using pressure perturbation. As the active sites are located at the interfaces between monomers, enzyme activity is directly related to the integrity of the tetramer. The effect of hydrostatic pressure on the enzyme was investigated by x-ray crystallography, small-angle x-ray scattering, and fluorescence spectroscopy. Enzymatic activity was also measured under pressure and after decompression. A global model, consistent with all measurements, discloses structural and functional details of the pressure-induced dissociation of the tetramer. Before dissociating, the pressurized protein adopts a conformational substate characterized by an expansion of its substrate binding pocket at the expense of a large neighboring hydrophobic cavity. This substate should be adopted by the enzyme during its catalytic mechanism, where the active site has to accommodate larger intermediates and product. The approach, combining several high-pressure techniques, offers a new (to our knowledge) means of exploring structural and functional properties of transient states relevant to protein mechanisms.

    Organizational Affiliation: 

    Institut de Biologie Structurale J.-P. Ebel UMR 5075 CEA CNRS UJF, Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uricase
A
302Aspergillus flavusMutation(s): 0 
Gene Names: uaZ (uox)
EC: 1.7.3.3
Find proteins for Q00511 (Aspergillus flavus)
Go to UniProtKB:  Q00511
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
AZA
Query on AZA
Download SDF File 
Download CCD File 
A
8-AZAXANTHINE
C4 H3 N5 O2
KVGVQTOQSNJTJI-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.182 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 79.700α = 90.00
b = 95.870β = 90.00
c = 104.990γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
REFMACphasing
SCALAdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
specdata collection

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-02-19
    Type: Database references