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Structure of IDP90922

Crystal Structure of Type I 3-Dehydroquinate Dehydratase (aroD) fromSalmonella typhimurium with close loop conformation.

Edit deposit information
CSGID target
IDP90922 
PDB Id
3OEX (NCBI MMDB
Authors
G.Minasov,S.H.Light,L.Shuvalova,L.Papazisi,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
George Minasov 
Responsible lab
Northwestern University 
Deposition Date
Aug 13, 2010 
Release Date
Sep 01, 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. While previously reported type I dehydroquinate dehydratase structures have reliably displayed an open and/or disordered behavior in apo structures and an ordered and closed behavior in ligand bound structures, this structure displays the unusual property of a closed loop despite the absence of ligand. An examination of crystal packing reveals that an open conformation of the loop would clash with crystal contacts, implicating crystal packing in biasing the loop to a closed conformation. In this structure we find that a chloride atom from the crystallization solution is bound precisely where the substrate‚Äôs carboxylate is found in the ligand bound structures. This finding suggests that the protein has a general ability to coordinate anionic species to this position and provides a basis for previous reports of chloride acting as a competitive inhibitor type I dehydroquinate dehydration.  
Functional assignment
 

Ligands

Ligand code Name Ligand type
CL CHLORIDE ION

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=64.15Å, b=75.76Å, c=94.26Å
α=90.00, β=102.65, γ=90.00 
Solvent content
39.17  
Matthews coefficient
2.02  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.53-1.90Å (1.95-1.90Å)  
Rall(%)
15.4 
Rwork(%)
15.2 (18.8) 
Rfree(%)
20.4 (24.6) 
Num. observed reflections
69236 (5004) 
Num. Rfree reflections
3531 (227) 
Completeness(%)
99.8 (97.7) 

Model parameters

Num Atoms
7994  
Num Waters
887  
Num Hetatoms
916  
Model mean isotropic B factor
17.990Å2  
RMSD bond length
0.014Å  
RMSD bond angle
1.431°  
Filename uploaded
rcsb061029.pdb (uploaded on Sep 14, 2010 5:35 PM)  
Inserted
Sep 14, 2010