4FML

Catalytic domain of VahC from Aeromonas hydrophila


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Characterization of an actin-targeting ADP-ribosyltransferase from Aeromonas hydrophila.

Shniffer, A.Visschedyk, D.D.Ravulapalli, R.Suarez, G.Turgeon, Z.J.Petrie, A.A.Chopra, A.K.Merrill, A.R.

(2012) J Biol Chem 287: 37030-37041

  • DOI: https://doi.org/10.1074/jbc.M112.397612
  • Primary Citation of Related Structures:  
    4FML

  • PubMed Abstract: 

    The mono-ADP-ribosyltransferase (mART) toxins are contributing factors to a number of human diseases, including cholera, diphtheria, traveler's diarrhea, and whooping cough. VahC is a cytotoxic, actin-targeting mART from Aeromonas hydrophila PPD134/91. This bacterium is implicated primarily in diseases among freshwater fish species but also contributes to gastrointestinal and extraintestinal infections in humans. VahC was shown to ADP-ribosylate Arg-177 of actin, and the kinetic parameters were K(m)(NAD(+)) = 6 μM, K(m)(actin) = 24 μM, and k(cat) = 22 s(-1). VahC activity caused depolymerization of actin filaments, which induced caspase-mediated apoptosis in HeLa Tet-Off cells. Alanine-scanning mutagenesis of predicted catalytic residues showed the predicted loss of in vitro mART activity and cytotoxicity. Bioinformatic and kinetic analysis also identified three residues in the active site loop that were critical for the catalytic mechanism. A 1.9 Å crystal structure supported the proposed roles of these residues and their conserved nature among toxin homologues. Several small molecules were characterized as inhibitors of in vitro VahC mART activity and suramin was the best inhibitor (IC(50) = 20 μM). Inhibitor activity was also characterized against two other actin-targeting mART toxins. Notably, these inhibitors represent the first report of broad spectrum inhibition of actin-targeting mART toxins.


  • Organizational Affiliation

    Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VsdC
A, B, C
223Aeromonas hydrophilaMutation(s): 0 
Gene Names: VahCvsdC
UniProt
Find proteins for Q49TP5 (Aeromonas hydrophila)
Explore Q49TP5 
Go to UniProtKB:  Q49TP5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ49TP5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.1α = 90
b = 91.1β = 90
c = 303.37γ = 120
Software Package:
Software NamePurpose
MxDCdata collection
PHASERphasing
PHENIXrefinement
AutoProcessdata reduction
BESTdata reduction
pointlessdata scaling
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-19
    Type: Initial release
  • Version 1.1: 2013-01-02
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references