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Structure of IDP00736

Structure of Glucose 6-phosphate Isomerase from Staphylococcus aureus

Edit deposit information
CSGID target
IDP00736 
PDB Id
3FF1 (NCBI MMDB
Authors
S.M.Anderson,J.S.Brunzelle,O.Onopriyenko,S.Peterson,W.F.Anderson,A.Savchenko,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Spencer Anderson 
Responsible lab
Northwestern University 
Deposition Date
Dec 01, 2008 
Release Date
Feb 03, 2009 

Annotation

Description
Glucose 6-phosphate isomerase is a well study enzyme that catalyzes one of the first steps in the glycolysis pathway, conversion of glucose 6-phosphate to fructose 6-phosphate. The molecule acts as a homodimer with two active sites formed in the interface between monomers. Although there are two monomers in the asymmetric unit of this crystal form, this is not the biological dimer. The biological dimer can be created for both chains via symmetry operations. Glucose 6-phosphate isomerase from a variety of different organisms has been solved, such as Geobacillus stearothermophilus, Thermus thermophilus, Mus musculus and Homo sapiens. The bacterial examples have the best structural similarity with S. aureus glucose 6-phosphate isomerase, but it is a very well conserved enzyme and also aligns well with the human and mouse versions. The protein has been previously crystallized with a variety of substrate analogues and inhibitors, such as 6-phosphogluconic acid (2CXR), erythose-4-phosphate (1IRI), and n-bromoacetyl-aminoethyl phosphate (1C7Q). 10mM substrate was added to the mother liquor during crystallization. There is very weak electron density overlaying the location where the phosphate and attached carbon of substrate analogues bind, but the rest is disordered. One copy of a linear sugar could be visualized distant from the active site on the surface of the molecule. Chou, C.-C., Sun, Y.-J., Meng, M., Hsiao, C.. (2000) The crystal structure of phosphoglucose isomerase/autocrine motility factor/neuroleukin complexed with its carbohydrate phosphate inhibitors suggests its substrate/receptor recognition J.Biol.Chem. 275: 23154-23160  
Functional assignment
 

Ligands

Ligand code Name Ligand type
NA Sodium ion
G6Q glucose-6-phosphate biological
MSE modified residue

Structure information

Unit cell parameters

Space Group
P 41 21 2  
Unit Cell

a=163.27Å, b=163.27Å, c=103.73Å
α=90.00, β=90.00, γ=90.00 
Solvent content
64.21  
Matthews coefficient
3.44  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
46.22-1.65Å (1.69-1.65Å)  
Rall(%)
14.8 
Rwork(%)
14.6 (24.3) 
Rfree(%)
17.0 (25.4) 
Num. observed reflections
172654 (10178) 
Num. Rfree reflections
8632 (531) 
Completeness(%)
98.2 (83.5) 

Model parameters

Num Atoms
7048  
Num Waters
1405  
Num Hetatoms
1684  
Model mean isotropic B factor
19.400Å2  
RMSD bond length
0.019Å  
RMSD bond angle
1.621°  
RMSD dihedral angle
5.643°
 
Filename uploaded
3FF1.pdb (uploaded on Feb 13, 2009 3:07 PM)  
Inserted
Feb 13, 2009