1G98

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

• PDB DOI: https://doi.org/10.2210/pdb1G98/pdb

• Classification: ISOMERASE
• Organism(s): Oryctolagus cuniculus
• Mutation(s): No 


• Deposited: 2000-11-22 Released: 2001-06-01 
• Deposition Author(s): Jeffery, C.J., Hardre, R., Salmon, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.236 
• R-Value Work: 0.211 

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: 11327814 
• DOI: https://doi.org/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 1.9 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.

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Organizational Affiliation: 

Laboratory for Molecular Biology, MC567, Department of Biology, University of Illinois at Chicago, Chicago, IL 60607, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 126.15 kDa 
• Atom Count: 9,712 
• Modelled Residue Count: 1,110 
• Deposited Residue Count: 1,116 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOGLUCOSE ISOMERASE	A, B	558	Oryctolagus cuniculus	Mutation(s): 0  EC: 5.3.1.9
UniProt
Find proteins for Q9N1E2 (Oryctolagus cuniculus) Explore Q9N1E2  Go to UniProtKB:  Q9N1E2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PA5	C [auth A], D [auth B]	5-PHOSPHOARABINONIC ACID C5 H11 O9 P HNECGPFIYSOYHF-JJYYJPOSSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PA5	Binding MOAD:  1G98	Ki: 2000 (nM) from 1 assay(s)
	PDBBind:  1G98	Ki: 2000 (nM) from 1 assay(s)

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 = 82.829	α = 90
b = 116.554	β = 90
c = 271.824	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-06-01 
Deposition Author(s): Jeffery, C.J., Hardre, R., Salmon, L.

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
• Version 1.4: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description