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Structure of IDP00167

Crystal structure of pre-cleavage form of cysteine protease domain from Vibrio cholerae RtxA toxin

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CSGID target
IDP00167 
PDB Id
3FZY (NCBI MMDB) 
Authors
Shuvalova, L., Minasov, G., Prochazkova, K., Satchell, K.J.F., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID) 
Responsible person
Ludmilla Shuvalova 
Responsible lab
Northwestern University 
Deposition Date
Jan 26, 2009 
Release Date
Feb 17, 2009 

Annotation

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Description
Vibrio cholerae produces a large multifunctional protein that undergoes autoproteolytic processing catalyzed by its cysteine protease domain (CPD) to release the cytopathic domains within the eukaryotic host cell cytoplasm. The CPD is activated after translocation into the host cell by the binding of inositol hexaphosphate (InsP6, red in the picture). One of the sites of proteolysis is at the N-terminus of the CPD. X-Ray crystallographic structure determination of the pro-form of a catalytically inactive mutant (C3568S) CPD reveals the structural basis for the InsP6 activation and the mechanism of proteolytic processing. The 1.8Å crystal structure shows that the CPD is a caspase-like protein that has the leucine (purple) of its N-terminal cleavage site bound in a hydrophobic specificity pocket and the scissile peptide bond located between the serine that was substituted for the essential cysteine and the conserved histidine residue (both shown with magenta carbon atoms). The InsP6 activating ligand is bound by a number of positively charged lysine and arginine residues from the N-terminal region (blue), the main body of the CDP (yellow) and the C-terminal region (green). Related toxins with Cysteine Protease Domains, but other cytopathic domains, occur in a number of other gram-negative bacteria. 
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
    IHP inositol hexakisphosphate biological
    CL chloride ion
    UNX unknown atom or ion

    Structure information

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    Unit cell parameters

    Space Group
    P 21 21 21  
    Unit Cell

    a=46.05Å, b=66.37Å, c=137.96Å
    α=90.00, β=90.00, γ=90.00  
    Solvent content
    40.38  
    Matthews coefficient
    2.06  

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    23.67-1.95Å (2.00-1.95Å)  
    Rall(%)
    17.1  
    Rwork(%)
    16.9 (22.0)  
    Rfree(%)
    21.6 (25.7)  
    Num. observed reflections
    31516 (2248)  
    Num. Rfree reflections
    1575 (109)  
    Completeness(%)
    99.6 (98.1)  

    Model parameters

    Num Atoms
    3484  
    Num Waters
    313  
    Num Hetatoms
    406  
    Model mean isotropic B factor (Å2)
    32.050  
    RMSD bond length (Å)
    0.013  
    RMSD bond angle
    1.696°  
    Filename uploaded
    rcsb051248.pdb (uploaded on Feb 13, 2009 11:58 AM)  
    Inserted
    Feb 13, 2009