4LK4

Structure of Vibrio cholerae VesB protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Functional and Structural Characterization of Vibrio cholerae Extracellular Serine Protease B, VesB.

Gadwal, S.Korotkov, K.V.Delarosa, J.R.Hol, W.G.Sandkvist, M.

(2014) J.Biol.Chem. 289: 8288-8298

  • DOI: 10.1074/jbc.M113.525261

  • PubMed Abstract: 
  • The chymotrypsin subfamily A of serine proteases consists primarily of eukaryotic proteases, including only a few proteases of bacterial origin. VesB, a newly identified serine protease that is secreted by the type II secretion system in Vibrio chole ...

    The chymotrypsin subfamily A of serine proteases consists primarily of eukaryotic proteases, including only a few proteases of bacterial origin. VesB, a newly identified serine protease that is secreted by the type II secretion system in Vibrio cholerae, belongs to this subfamily. VesB is likely produced as a zymogen because sequence alignment with trypsinogen identified a putative cleavage site for activation and a catalytic triad, His-Asp-Ser. Using synthetic peptides, VesB efficiently cleaved a trypsin substrate, but not chymotrypsin and elastase substrates. The reversible serine protease inhibitor, benzamidine, inhibited VesB and served as an immobilized ligand for VesB affinity purification, further indicating its relationship with trypsin-like enzymes. Consistent with this family of serine proteases, N-terminal sequencing implied that the propeptide is removed in the secreted form of VesB. Separate mutagenesis of the activation site and catalytic serine rendered VesB inactive, confirming the importance of these features for activity, but not for secretion. Similar to trypsin but, in contrast to thrombin and other coagulation factors, Na(+) did not stimulate the activity of VesB, despite containing the Tyr(250) signature. The crystal structure of catalytically inactive pro-VesB revealed that the protease domain is structurally similar to trypsinogen. The C-terminal domain of VesB was found to adopt an immunoglobulin (Ig)-fold that is structurally homologous to Ig-folds of other extracellular Vibrio proteins. Possible roles of the Ig-fold domain in stability, substrate specificity, cell surface association, and type II secretion of VesB, the first bacterial multidomain trypsin-like protease with known structure, are discussed.


    Organizational Affiliation

    From the Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109 and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VESB protease
A
357Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)Mutation(s): 1 
Find proteins for Q9KSQ6 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Go to UniProtKB:  Q9KSQ6
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.187 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 121.570α = 90.00
b = 121.570β = 90.00
c = 71.310γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
XSCALEdata scaling
XDSdata reduction
BOSdata collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2014-04-09
    Type: Database references