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 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/10.1006/jmbi.1999.2566
  • Primary Citation of Related Structures:  
    5PGM

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOSPHOGLYCERATE MUTASE 1246Saccharomyces cerevisiaeMutation(s): 0 
EC: 5.4.2.1 (PDB Primary Data), 5.4.2.11 (UniProt)
UniProt
Find proteins for P00950 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00950 
Go to UniProtKB:  P00950
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00950
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth D]
J [auth D]
K [auth C]
L [auth C]
M [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ALA
Query on ALA

Download Ideal Coordinates CCD File 
S [auth E]ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-08-09
    Changes: Database references, Derived calculations, Other, Refinement description