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Structure of IDP90626

1.02 Angstrom resolution crystal structure of 3-phosphoshikimate 1- carboxyvinyltransferase from Vibrio cholerae in complex with shikimate-3-phosphate (partially photolyzed) and glyphosate.

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CSGID target
IDP90626 
PDB Id
3NVS (NCBI MMDB) 
Authors
G.Minasov, S.H.Light, A.Halavaty, G.Shuvalova, L.Papazisi, W.F.Anderson, Center for Structural Genomics of Infectious Diseases (CSGID) 
Responsible person
George Minasov 
Responsible lab
Northwestern University 
Deposition Date
Jul 08, 2010 
Release Date
Jul 21, 2010 

Annotation

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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. 3-phosphoshikimate 1- carboxyvinyltransferase is the sixth enzyme in the shikimate pathway and catalyzes the conversion of shikimate-3-phosphate and phosphoenolpyruvate to 5-enolpyruvyl-3-shikimate phosphate. This protein was co-crystallized with the substrate shikimate-3-phosphate and the commercially successful herbicide glyphosate. The enzyme consists of six βαβαββ motifs, three in both N- and C-terminal domains. The ultrahigh resolution of this structure provides an exquisite view of the mode of shikimate-3-phosphate and glyphosate binding. Glyphosate is observed to bind adjacent to shikimate-3-phosphate in phosphoenolpyruvate’s binding site.  
Functional assignment
 
Slides:
  • Asymmetric unit
  • Biological unit
  • B-factors distribution
  • B-factors distribution on the surface
  • Homolog superposition
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    secondary structure, N to C, molecule

    Ligands

    Ligand code Name Ligand type
    S3P shikimate-3-phosphate biological
    GPJ glyphosate biological
    MG unknown
    CL chloride ion
    EPE 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid
    PO4 phosphate ion
    SKM (3r,4s,5r)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid

    Structure information

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    Unit cell parameters

    Space Group
    P 1 21 1  
    Unit Cell

    a=43.87Å, b=87.48Å, c=49.99Å
    α=90.00, β=105.26, γ=90.00  
    Solvent content
    35.02  
    Matthews coefficient
    1.89  

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    14.89-1.02Å (1.05-1.02Å)  
    Rall(%)
    11.5  
    Rwork(%)
    11.4 (21.3)  
    Rfree(%)
    13.8 (23.5)  
    Num. observed reflections
    178385 (12825)  
    Num. Rfree reflections
    8919 (620)  
    Completeness(%)
    97.2 (95.3)  

    Model parameters

    Num Atoms
    3632  
    Num Waters
    747  
    Num Hetatoms
    905  
    Model mean isotropic B factor (Å2)
    8.510  
    RMSD bond length (Å)
    0.011  
    RMSD bond angle
    1.542°  
    Filename uploaded
    rcsb060340.pdb (uploaded on Jul 13, 2010 5:55 PM)  
    Inserted
    Jul 13, 2010