Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 125.92 kDa 
• Atom Count: 9711 
• Modelled Residue Count: 1112 
• Deposited Residue Count: 1114 
• Unique protein chains: 1

1KOJ

Crystal structure of rabbit phosphoglucose isomerase complexed with 5-phospho-D-arabinonohydroxamic acid

• PDB DOI: 10.2210/pdb1KOJ/pdb

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


• Deposited: 2001-12-20 Released: 2002-05-03 
• Deposition Author(s): Arsenieva, D., Hardre, R., Salmon, L., Jeffery, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.254 
• R-Value Work: 0.220 
• R-Value Observed: 0.223 

Literature

The crystal structure of rabbit phosphoglucose isomerase complexed with 5-phospho-D-arabinonohydroxamic acid.

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

(2002) Proc Natl Acad Sci U S A 99: 5872-5877

• PubMed: 11983887 
• DOI: 10.1073/pnas.052131799
• Primary Citation of Related Structures:  
  1KOJ


• PubMed Abstract: 
  

Phosphoglucose isomerase (EC ) catalyzes the second step in glycolysis, the reversible isomerization of D-glucose 6-phosphate to D-fructose 6-phosphate. The reaction mechanism involves acid-base catalysis with proton transfer and proceeds through a cis-enediol(ate) intermediate. 5-Phospho-D-arabinonohydroxamic acid (5PAH) is a synthetic small molecule that resembles the reaction intermediate, differing only in that it has a nitrogen atom in place of C1. Hence, 5PAH is the best inhibitor of the isomerization reaction reported to date with a K(i) of 2 x 10(-7) M. Here we report the crystal structure of rabbit phosphoglucose isomerase complexed with 5PAH at 1.9 A resolution. The interaction of 5PAH with amino acid residues in the enzyme active site supports a model of the catalytic mechanism in which Glu-357 transfers a proton between C1 and C2 and Arg-272 helps stabilize the intermediate. It also suggests a mechanism for proton transfer between O1 and O2.

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Organizational Affiliation: 

Laboratory for Molecular Biology, MC567, Department of Biological Sciences, University of Illinois, Chicago, IL 60607, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-6-phosphate isomerase	A, B	557	Oryctolagus cuniculus	Mutation(s): 0  Gene Names: GPI 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
PAN	C [auth A], D [auth B]	5-PHOSPHO-D-ARABINOHYDROXAMIC ACID C5 H12 N O9 P OHQFMJPEBPCIEQ-JJYYJPOSSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PAN	PDBBind:  1KOJ	Ki: 200 (nM) from 1 assay(s)
	BindingDB:  1KOJ	Ki: 100 (nM) from 1 assay(s)
	Binding MOAD:  1KOJ	Ki: 200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.254 
• R-Value Work: 0.220 
• R-Value Observed: 0.223 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.69	α = 90
b = 115.97	β = 90
c = 271.85	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-12-20 
• Released Date: 2002-05-03 
Deposition Author(s): Arsenieva, D., Hardre, R., Salmon, L., Jeffery, C.J.

Revision History  

• Version 1.0: 2002-05-03
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance