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Structure of IDP01038

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium.

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CSGID target
IDP01038 
PDB Id
3GHZ (NCBI MMDB) 
Authors
J.Osipiuk,M.Gu,S.Peterson,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Jerzy Osipiuk 
Responsible lab
Argonne National Laboratory 
Deposition Date
Mar 04, 2009 
Release Date
Mar 17, 2009 

Annotation

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Description
2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase from Salmonella typhimurium, ispF gene product, takes part in biosynthesis of the isomers isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate, which are universal five-carbon precursors of isoprenoids. The enzyme is involved in the non-mevalonate pathway of isoprenoid synthesis which is essential in all organisms. The non-mevolanate route is used by many bacteria and human pathogens. This route appears to involve seven enzymes. MECDP synthetases, ispF and YgbB proteins, catalyze the fifth stage of the pathway. They convert 4-diphosphocytidyl-2C-methyl-D-erythritol-2-phosphate into MECDP and CMP. The enzyme is a homotrimer with three active sites located in a cleft lined by residues from two subunits. Each active site binds a Zn2+ ion and the ribose and diphosphate of CDP. The non-mevalonate pathway is present in many bacteria, some algae, certain protozoa, and in the plastids of higher plants, but not in mammals or archaea. Therefore, these enzymes have been recognised as promising drug targets. 
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
    GOL glycerol crystallization
    MG magnesium ion crystallization
    POP pyrophosphate 2- biological

    Structure information

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    Unit cell parameters

    Space Group
    I 2 3  
    Unit Cell

    a=143.97Å, b=143.97Å, c=143.97Å
    α=90.00, β=90.00, γ=90.00  
    Solvent content
    48.97  
    Matthews coefficient
    2.41  

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    46.00-2.03Å (2.08-2.03Å)  
    Rall(%)
    16.8  
    Rwork(%)
    16.6 (22.0)  
    Rfree(%)
    20.5 (25.4)  
    Num. observed reflections
    33851 (2369)  
    Num. Rfree reflections
    1726 (128)  
    Completeness(%)
    99.9 (99.8)  

    Model parameters

    Num Atoms
    3591  
    Num Waters
    198  
    Num Hetatoms
    232  
    Model mean isotropic B factor (Å2)
    32.010  
    RMSD bond length (Å)
    0.018  
    RMSD bond angle
    1.644°  
    Filename uploaded
    rcsb051883.pdb (uploaded on Mar 09, 2009 5:42 PM)  
    Inserted
    Mar 09, 2009