1XTZ

Crystal structure of the S. cerevisiae D-ribose-5-phosphate isomerase: comparison with the archeal and bacterial enzymes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the S. cerevisiae D-ribose-5-phosphate isomerase: comparison with the archaeal and bacterial enzymes

Graille, M.Meyer, P.Leulliot, N.Sorel, I.Janin, J.Van Tilbeurgh, H.Quevillon-Cheruel, S.

(2005) Biochimie 87: 763-769

  • DOI: 10.1016/j.biochi.2005.03.001
  • Primary Citation of Related Structures:  
    1XTZ

  • PubMed Abstract: 
  • Ribose-5-phosphate isomerase A has an important role in sugar metabolism by interconverting ribose-5-phosphate and ribulose-5-phosphate. This enzyme is ubiquitous and highly conserved among the three kingdoms of life. We have solved the 2.1 A resolution crystal structure of the Saccharomyces cerevisiae enzyme by molecular replacement ...

    Ribose-5-phosphate isomerase A has an important role in sugar metabolism by interconverting ribose-5-phosphate and ribulose-5-phosphate. This enzyme is ubiquitous and highly conserved among the three kingdoms of life. We have solved the 2.1 A resolution crystal structure of the Saccharomyces cerevisiae enzyme by molecular replacement. This protein adopts the same fold as its archaeal and bacterial orthologs with two alpha/beta domains tightly packed together. Mapping of conserved residues at the surface of the protein reveals strong invariability of the active site pocket, suggesting a common ligand binding mode and a similar catalytic mechanism. The yeast enzyme associates as a homotetramer similarly to the archaeal protein. The effect of an inactivating mutation (Arg189 to Lys) is discussed in view of the information brought by this structure.


    Organizational Affiliation

    Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, CNRS-UMR 8619, Université Paris-Sud, Bâtiment 430, 91405 Orsay, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribose-5-phosphate isomeraseA264Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RKI1
EC: 5.3.1.6
Find proteins for Q12189 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12189 
Go to UniProtKB:  Q12189
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.24α = 90
b = 209.24β = 90
c = 209.24γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling
BEASTphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-30
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description