1G98

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 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

  • DOI: 10.1021/bi0018483
  • Primary Citation of Related Structures:  
    1G98

  • 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 inhibitor of isomerase activity, 5-phospho-D-arabinonate (5PAA), at 1 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOSPHOGLUCOSE ISOMERASEAB558Oryctolagus cuniculusMutation(s): 0 
Gene Names: GPI
EC: 5.3.1.9
Find proteins for Q9N1E2 (Oryctolagus cuniculus)
Explore Q9N1E2 
Go to UniProtKB:  Q9N1E2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PA5
Query on PA5

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  Binding MOAD
PA5Ki :  2000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 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
b = 116.554β = 90
c = 271.824γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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