1BQ3

SACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE IN COMPLEX WITH INOSITOL HEXAKISPHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Polyanionic inhibitors of phosphoglycerate mutase: combined structural and biochemical analysis.

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

(1999) J Mol Biol 289: 691-699

  • DOI: 10.1006/jmbi.1999.2848
  • Primary Citation of Related Structures:  
    1BQ3, 1BQ4

  • PubMed Abstract: 
  • The effects that the inhibitors inositol hexakisphosphate and benzene tri-, tetra- and hexacarboxylates have on the phosphoglycerate mutases from Saccharomyces cerevisiae and Schizosaccharomyces pombe have been determined. Their Kivalues have been calculated, and the ability of the inhibitors to protect the enzymes against limited proteolysis investigated ...

    The effects that the inhibitors inositol hexakisphosphate and benzene tri-, tetra- and hexacarboxylates have on the phosphoglycerate mutases from Saccharomyces cerevisiae and Schizosaccharomyces pombe have been determined. Their Kivalues have been calculated, and the ability of the inhibitors to protect the enzymes against limited proteolysis investigated. These biochemical data have been placed in a structural context by the solution of the crystal structures of S. cerevisiae phosphoglycerate mutase soaked with inositol hexakisphosphate or benzene hexacarboxylate. These large polyanionic compounds bind to the enzyme so as to block the entrance to the active-site cleft. They form multiple interactions with the enzyme, consistent with their low Kivalues, and afford good protection against limited proteolysis of the C-terminal region by thermolysin. The inositol compound is more efficacious because of its greater number of negative charges. The S. pombe phosphoglycerate mutase that is inherently lacking a comparable C-terminal region has higher Kivalues for the compounds tested. Moreover, the S. pombe enzyme is less sensititive to proteolysis, and the presence or absence of the inhibitor molecules has little effect on susceptibility to proteolysis.


    Related Citations: 
    • 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., Phillips, S.E.V.P., Fothergill-Gilmore, L.A.
      (1999) J Mol Biol 286: 1507
    • The 2.3 Angstroms X-Ray Structure of S.Cerevisiae Phosphoglycerate Mutase
      Rigden, D.J., Alexeev, D., Phillips, S.E.V.P., Fothergill-Gilmore, L.A.
      (1998) J Mol Biol 276: 449

    Organizational Affiliation

    School of Biochemistry and Molecular Biology, University of Leeds, Leeds, LS2 9JT, England.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (PHOSPHOGLYCERATE MUTASE 1)C [auth A], D [auth B], B [auth C], A [auth D]246Saccharomyces 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
IHP PDBBind:  1BQ3 Ki: 4000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.58α = 90
b = 93.38β = 90.13
c = 148.56γ = 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  (Full details and data files)

  • Version 1.0: 1998-08-26
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-10-14
    Changes: Derived calculations, Structure summary