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Structure of IDP90224

Structure of the type III effector/phosphothreonine lyase OspF from Shigella flexneri

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CSGID target
IDP90224 
PDB Id
3I0U (NCBI MMDB) 
Authors
Singer A.U., Skarina T., Nocek B., Gordon R., Lam R., Kagan O., Edwards A.M., Joachimiak A., Chirgadze N.Y., Anderson W.F., Savchenko A., Center for Structural Genomics of Infectious Diseases (CSGID) 
Responsible person
Alexander Singer 
Responsible lab
University of Toronto 
Deposition Date
Jun 25, 2009 
Release Date
Sep 01, 2009 

Annotation

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Description
Gram-negative pathogens exert virulence to a significant degree by the secretion of toxins, termed effectors, through the type III secretion system. One effector from Salmonella sp., SpvC, was found to have a highly novel enzymatic function, irreversibly dephosphorylating an activating threonine residue on MAP kinase proteins via a lyase activity (phosphothreonine lyase), leaving a double bond between the alpha and beta carbon (Science. 2007 315:1000-3.). We have solved the structure of the homologue of SpvC from Shigella flexneri, termed OspF, to 2.7 Å, from residue 23 to the C-terminus. This structure shows a very similar overall fold to Salmonella enterica SpvC, to which it shares 64% sequence identity. The principal difference involves a change in direction in the most N-terminal helix, which folds around the structure in SpvC but which remains straight in OspF. The overall significance of this finding has yet to be determined. Although 2 molecules of OspF can be found in an asymmetric unit in crystals, the protein is predicted to be monomeric. 
Functional assignment
phosphothreonince lyase 
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
    MPD (4S)-2-methyl-2,4-pentanediol

    Structure information

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    Unit cell parameters

    Space Group
    P 41 21 2  
    Unit Cell

    a=62.12Å, b=62.12Å, c=239.59Å
    α=90.00, β=90.00, γ=90.00  
    Solvent content
    45.9  
    Matthews coefficient
    2.27  

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    43.94-2.70Å (2.77-2.70Å)  
    Rall(%)
    25.2  
    Rwork(%)
    25.0 (26.4)  
    Rfree(%)
    28.7 (33.3)  
    Num. observed reflections
    13700 (963)  
    Num. Rfree reflections
    671 (43)  
    Completeness(%)
    99.8 (100.0)  

    Model parameters

    Num Atoms
    3193  
    Num Waters
    6  
    Num Hetatoms
    14  
    Model mean isotropic B factor (Å2)
    71.020  
    RMSD bond length (Å)
    0.017  
    RMSD bond angle
    1.713°  
    Filename uploaded
    rcsb053822_final.pdb (uploaded on Oct 05, 2009 11:47 AM)  
    Inserted
    Oct 05, 2009