5ECW

Structure of the Shigella flexneri VapC mutant D7A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of the active site architecture of the VapC toxin from Shigella flexneri.

Xu, K.Dedic, E.Brodersen, D.E.

(2016) Proteins 84: 892-899

  • DOI: 10.1002/prot.25002
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The VapC toxin from the Shigella flexneri 2a virulence plasmid pMYSH6000 belongs to the PIN domain protein family, which is characterized by a conserved fold with low amino acid sequence conservation. The toxin is a bona fide Mg(2+) -dependent ribonu ...

    The VapC toxin from the Shigella flexneri 2a virulence plasmid pMYSH6000 belongs to the PIN domain protein family, which is characterized by a conserved fold with low amino acid sequence conservation. The toxin is a bona fide Mg(2+) -dependent ribonuclease and has been shown to target initiator tRNA(fMet) in vivo. Here, we present crystal structures of active site catalytic triad mutants D7A, D7N, and D98N of the VapC toxin in absence of antitoxin. In all structures, as well as in solution, VapC forms a dimer. In the D98N structure, a Hepes molecule occupies both active sites of the dimer and comparison with the structure of RNase H bound to a DNA/RNA hybrid suggests that the Hepes molecule mimics the position of an RNA nucleotide in the VapC active site. Proteins 2016; 84:892-899. © 2016 Wiley Periodicals, Inc.


    Organizational Affiliation

    Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, Aarhus C, DK-8000, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tRNA(fMet)-specific endonuclease VapC
A, B
138Shigella flexneriMutation(s): 1 
Gene Names: vapC (mvpA, stborf2)
EC: 3.1.-.-
Find proteins for O06662 (Shigella flexneri)
Go to UniProtKB:  O06662
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.189 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 120.100α = 90.00
b = 120.100β = 90.00
c = 52.530γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Scholarship CouncilChina--

Revision History 

  • Version 1.0: 2016-02-17
    Type: Initial release
  • Version 1.1: 2016-06-15
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Data collection