2GC1

The crystal structure of phosphoglucose isomerase from Pyrococcus furiosus in complex with sorbitol 6-phosphate and zinc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Evidence Supporting a cis-enediol-based Mechanism for Pyrococcus furiosus Phosphoglucose Isomerase

Berrisford, J.M.Hounslow, A.M.Akerboom, J.Hagen, W.R.Brouns, S.J.van der Oost, J.Murray, I.A.Michael Blackburn, G.Waltho, J.P.Rice, D.W.Baker, P.J.

(2006) J.Mol.Biol. 358: 1353-1366

  • DOI: 10.1016/j.jmb.2006.03.015
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The enzymatic aldose ketose isomerisation of glucose and fructose sugars involves the transfer of a hydrogen between their C1 and C2 carbon atoms and, in principle, can proceed through either a direct hydride shift or via a cis-enediol intermediate. ...

    The enzymatic aldose ketose isomerisation of glucose and fructose sugars involves the transfer of a hydrogen between their C1 and C2 carbon atoms and, in principle, can proceed through either a direct hydride shift or via a cis-enediol intermediate. Pyrococcus furiosus phosphoglucose isomerase (PfPGI), an archaeal metalloenzyme, which catalyses the interconversion of glucose 6-phosphate and fructose 6-phosphate, has been suggested to operate via a hydride shift mechanism. In contrast, the structurally distinct PGIs of eukaryotic or bacterial origin are thought to catalyse isomerisation via a cis-enediol intermediate. We have shown by NMR that hydrogen exchange between substrate and solvent occurs during the reaction catalysed by PfPGI eliminating the possibility of a hydride-shift-based mechanism. In addition, kinetic measurements on this enzyme have shown that 5-phospho-d-arabinonohydroxamate, a stable analogue of the putative cis-enediol intermediate, is the most potent inhibitor of the enzyme yet discovered. Furthermore, determination and analysis of crystal structures of PfPGI with bound zinc and the substrate F6P, and with a number of competitive inhibitors, and EPR analysis of the coordination of the metal ion within PfPGI, have suggested that a cis-enediol intermediate-based mechanism is used by PfPGI with Glu97 acting as the catalytic base responsible for isomerisation.


    Organizational Affiliation

    The Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucose-6-phosphate isomerase
A, B
188Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: pgiA
EC: 5.3.1.9
Find proteins for P83194 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  P83194
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
S6P
Query on S6P

Download SDF File 
Download CCD File 
A, B
D-SORBITOL-6-PHOSPHATE
1-O-PHOSPHONO-D-GLUCITOL, D-GLUCITOL-6-PHOSPHATE
C6 H15 O9 P
GACTWZZMVMUKNG-SLPGGIOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.311α = 90.00
b = 72.857β = 103.57
c = 71.640γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
CCP4data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-11
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance