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Structure of IDP90922

1.03 Angstrom Crystal Structure of Q236A Mutant Type I Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium

Edit deposit information
CSGID target
IDP90922 
PDB Id
3O1N (NCBI MMDB
Authors
S.H.Light,G.Minasov,L.Shuvalova,L.Papazisi,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Sam Light 
Responsible lab
Northwestern University 
Deposition Date
Jul 21, 2010 
Release Date
Aug 11, 2010 

Annotation

Description
The shikimate pathway links metabolism of carbohydrates to biosynthesis of aromatic compounds. In a sequence of seven steps, phosphoenolpyruvate and erythrose 4-phosphate are converted to chorismate, a precursor of the aromatic amino acids and many secondary aromatic metabolites. The shikimate pathway is essential for most bacteria and plants but absent in humans, making it an attractive target for the development of novel antibiotics. The third step in the pathway consists of the dehydration of dehydroquinate to dehydroshikimate. This reaction can be catalyzed by two enzyme families which utilize distinct mechanisms. The protein structure presented here is representative of the type I enzyme family. A comparison of apo and reaction intermediate bound structures (PDB codes 3L2I and 3M7W) reveals a surface loop which is observed to close over the active upon substrate binding. The loop residue glutamine-236 is highly and conserved across species, implying that the residue may be functionally significant. To address the function of the loop we mutated glutamine-236 to alanine. The glutamine-236 to alanine mutant has profoundly deficient kinetics. This crystal structure reveals that loop closure in the mutant enzyme fails to relocate the residue arginine-214 – which is important in binding the substrate’s carboxylate - to its observed substrate binding position. Thus, this structure provides insight into the role of the loop and glutamine-236 in protein function.  
Functional assignment
dehydroquinate dehydratase 

Ligands

Ligand code Name Ligand type
CL
MG

Structure information

Unit cell parameters

Space Group
P 1  
Unit Cell

a=45.43Å, b=46.48Å, c=55.79Å
α=104.23, β=97.50, γ=98.70 
Solvent content
33.49  
Matthews coefficient
1.85  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
26.62-1.03Å (1.06-1.03Å)  
Rall(%)
14.1 
Rwork(%)
14.0 (17.5) 
Rfree(%)
16.2 (18.5) 
Num. observed reflections
196962 (13252) 
Num. Rfree reflections
9848 (666) 
Completeness(%)
92.6 (84.5) 

Model parameters

Num Atoms
4097  
Num Waters
775  
Num Hetatoms
854  
Model mean isotropic B factor
10.930Å2  
RMSD bond length
0.012Å  
RMSD bond angle
1.464°  
Filename uploaded
rcsb060551.pdb (uploaded on Aug 16, 2010 3:53 PM)  
Inserted
Aug 16, 2010