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: 2.1 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


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

  • 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 resolut ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribose-5-phosphate isomerase
A
264Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RKI1
EC: 5.3.1.6
Find proteins for Q12189 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12189
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.193 
  • Space Group: F 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 209.240α = 90.00
b = 209.240β = 90.00
c = 209.240γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
BEASTphasing
REFMACrefinement
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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