1G98

CRYSTAL STRUCTURE ANALYSIS OF RABBIT PHOSPHOGLUCOSE ISOMERASE COMPLEXED WITH 5-PHOSPHOARABINONATE, A TRANSITION STATE ANALOGUE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of rabbit phosphoglucose isomerase complexed with 5-phospho-D-arabinonate identifies the role of Glu357 in catalysis.

Jeffery, C.J.Hardre, R.Salmon, L.

(2001) Biochemistry 40: 1560-1566


  • PubMed Abstract: 
  • Phosphoglucose isomerase (PGI; E.C. 5.3.1.9) catalyzes the second step in glycolysis, the interconversion of D-glucose-6-phosphate and D-fructose-6-phosphate. We determined the X-ray crystal structure of rabbit PGI complexed with a competitive inhibi ...

    Phosphoglucose isomerase (PGI; E.C. 5.3.1.9) catalyzes the second step in glycolysis, the interconversion of D-glucose-6-phosphate and D-fructose-6-phosphate. We determined the X-ray crystal structure of rabbit PGI complexed with a competitive inhibitor of isomerase activity, 5-phospho-D-arabinonate (5PAA), at 1.9 A resolution. 5PAA is a better mimic of the proposed cis-enediol(ate) intermediate than 6-phospho-D-gluconate, which was used in a previously reported crystal structure of rabbit PGI. The orientation of 5PAA bound in the enzyme active site predicts that active site residue Glu357 is the residue that transfers a proton between C2 and C1 of the proposed cis-enediol(ate) intermediate. Amino acid residues Arg272 and Lys210 are predicted to be involved in stabilizing the negative charge of the intermediate.


    Organizational Affiliation

    Laboratory for Molecular Biology, MC567, Department of Biology, University of Illinois at Chicago, Chicago, IL 60607, USA. cjeffery@uic.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOGLUCOSE ISOMERASE
A, B
558Oryctolagus cuniculusGene Names: GPI
EC: 5.3.1.9
Find proteins for Q9N1E2 (Oryctolagus cuniculus)
Go to Gene View: GPI
Go to UniProtKB:  Q9N1E2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PA5
Query on PA5

Download SDF File 
Download CCD File 
A, B
5-PHOSPHOARABINONIC ACID
C5 H11 O9 P
HNECGPFIYSOYHF-JJYYJPOSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PA5Ki: 2000 nM BINDINGMOAD
PA5Ki: 2000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.211 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 82.829α = 90.00
b = 116.554β = 90.00
c = 271.824γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-06-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model