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Structure of IDP90163

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

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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

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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 
Slides:
  • Asymmetric unit
  • Biological unit
  • B-factors distribution
  • B-factors distribution on the surface
  • Homolog superposition
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    Ligands

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

    Structure information

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    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 (Å2)
    21.950  
    RMSD bond length (Å)
    0.012  
    RMSD bond angle
    1.537°  
    Filename uploaded
    rcsb055088.pdb (uploaded on Sep 11, 2009 7:25 PM)  
    Inserted
    Sep 11, 2009