5PGM

SACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Sulphate ions observed in the 2.12 A structure of a new crystal form of S. cerevisiae phosphoglycerate mutase provide insights into understanding the catalytic mechanism.

Rigden, D.J.Walter, R.A.Phillips, S.E.Fothergill-Gilmore, L.A.

(1999) J Mol Biol 286: 1507-1517

  • DOI: 10.1006/jmbi.1999.2566
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The structure of a new crystal form of Saccharomyces cerevisiae phosphoglycerate mutase has been solved and refined to 2.12 A with working and free R-factors of 19.7 and 22.9 %, respectively. Higher-resolution data and greater non-crystallographic sy ...

    The structure of a new crystal form of Saccharomyces cerevisiae phosphoglycerate mutase has been solved and refined to 2.12 A with working and free R-factors of 19.7 and 22.9 %, respectively. Higher-resolution data and greater non-crystallographic symmetry have produced a more accurate protein structure than previously. Prominent among the differences from the previous structure is the presence of two sulphate ions within each active site cleft. The separation of the sulphates suggests that they may occupy the same sites as phospho groups of the bisphosphate ligands of the enzyme. Plausible binding modes for 2,3-bisphosphoglycerate and 1, 3-bisphosphoglycerate are thereby suggested. These results support previous conclusions from mutant studies, highlight interesting new targets for mutagenesis and suggest a possible mechanism of enzyme phosphorylation.


    Related Citations: 
    • The 2.3 A X-Ray Crystal Structure of S. Cerevisiae Phosphoglycerate Mutase
      Rigden, D.J., Alexeev, D., Phillips, S.E., Fothergill-Gilmore, L.A.
      (1998) J Mol Biol 276: 449
    • Structure of Yeast Phosphoglycerate Mutase
      Campbell, J.W., Watson, H.C., Hodgson, G.I.
      (1974) Nature 250: 301

    Organizational Affiliation

    School of Biochemistry and Molecular Biology, Astbury Building, University of Leeds, Leeds, LS2 9JT, UK.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOGLYCERATE MUTASE 1
A, B, C, D, E, F, G, H
246Saccharomyces cerevisiaeMutation(s): 0 
EC: 5.4.2.1 (PDB Primary Data), 5.4.2.11 (UniProt)
Find proteins for P00950 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00950
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B, C, D, E, F, G, H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ALA
Query on ALA

Download CCD File 
E
ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.497α = 90
b = 93.262β = 90.15
c = 147.329γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-02-16
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance