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Structure of IDP90163

Crystal Structure of Type I 3-Dehydroquinate Dehydratase (aroD) from Clostridium difficile with Covalent Reaction Intermediate.

Edit deposit information
CSGID target
IDP90163 
PDB Id
3JS3 (NCBI MMDB
Authors
G.Minasov,S.H.Light,L.Shuvalova,I.Dubrovska,J.Winsor,S.N.Peterson,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
George Minasov 
Responsible lab
Northwestern University 
Deposition Date
Sep 09, 2009 
Release Date
Sep 22, 2009 

Annotation

Description
The shikimate pathway links metabolism of carbohydrates to biosynthesis of aromatic compounds. In a sequence of seven metabolic steps, phosphoenolpyruvate and erythrose 4-phosphate are converted to chorismate, the precursor of the aromatic amino acids and many secondary aromatic metabolites. The shikimate pathway is essential for most bacteria and plants but absent in animals.The dehydration of dehydroquinate to dehydroshikimate is an essential step in the shikimate pathway and is thus an attractive target for the development of novel antibiotics. In the pharmaceutical industry, shikimic acid from the Chinese star anise is used as a base material for production of Tamiflu (oseltamivir). Two distinct types of dehydroquinate dehydratases have been shown to catalyze the dehydration of dehydroquinate through disparate mechanisms. The protein we studied is representative of the type I enzyme, which is known to form Schiff base with the reaction intermediate. It has a typical TIM barrel fold with eight parallel beta strands, and active site located at the C-terminal ends of strands. The protein was co-crystallized with the 3-dehydroshikimate, which was found covalently bound to the highly conserved lysine in the active site. The reported structure represents the intermediate step in the dehydration of dehydroquinate to dehydroshikimate.  
Functional assignment
3-dehydroquinate dehydratase 

Ligands

Ligand code Name Ligand type
DHS 3-amino-4,5-dihydroxy-cyclohex-1-enecarboxylate biological

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=60.47Å, b=139.62Å, c=66.77Å
α=90.00, β=90.63, γ=90.00 
Solvent content
49.05  
Matthews coefficient
2.41  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.55-2.20Å (2.26-2.20Å)  
Rall(%)
19.2 
Rwork(%)
18.9 (28.0) 
Rfree(%)
24.1 (33.0) 
Num. observed reflections
55907 (4028) 
Num. Rfree reflections
2851 (214) 
Completeness(%)
99.8 (98.0) 

Model parameters

Num Atoms
8116  
Num Waters
318  
Num Hetatoms
366  
Model mean isotropic B factor
21.950Å2  
RMSD bond length
0.012Å  
RMSD bond angle
1.537°  
Filename uploaded
rcsb055088.pdb (uploaded on Sep 11, 2009 7:25 PM)  
Inserted
Sep 11, 2009