1BQ4

SACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE IN COMPLEX WITH BENZENE HEXACARBOXYLATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • 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 ca ...

    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.,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.,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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (PHOSPHOGLYCERATE MUTASE 1)
D, C, A, B
246Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: GPM1 (GPM)
EC: 5.4.2.11
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 SDF File 
Download CCD File 
B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BHC
Query on BHC

Download SDF File 
Download CCD File 
A
BENZENE HEXACARBOXYLIC ACID
C12 H6 O12
YDSWCNNOKPMOTP-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BHCKi: 6000 nM BINDINGMOAD
BHCKi: 6000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 82.510α = 90.00
b = 92.520β = 90.00
c = 148.050γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
MOSFLMdata reduction
X-PLORrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-08-26
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance