3X0U

Crystal structure of PirB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The opportunistic marine pathogen Vibrio parahaemolyticus becomes virulent by acquiring a plasmid that expresses a deadly toxin

Lee, C.T.Chen, I.T.Yang, Y.T.Ko, T.P.Huang, Y.T.Huang, J.Y.Huang, M.F.Lin, S.J.Chen, C.Y.Lin, S.S.Lightner, D.V.Wang, H.C.Wang, A.H.J.Wang, H.C.Hor, L.I.Lo, C.F.

(2015) Proc Natl Acad Sci U S A 

  • DOI: 10.1073/pnas.1503129112
  • Primary Citation of Related Structures:  
    3X0T, 3X0U

  • PubMed Abstract: 
  • Acute hepatopancreatic necrosis disease (AHPND) is a severe, newly emergent penaeid shrimp disease caused by Vibrio parahaemolyticus that has already led to tremendous losses in the cultured shrimp industry. Until now, its disease-causing mechanism has remained unclear ...

    Acute hepatopancreatic necrosis disease (AHPND) is a severe, newly emergent penaeid shrimp disease caused by Vibrio parahaemolyticus that has already led to tremendous losses in the cultured shrimp industry. Until now, its disease-causing mechanism has remained unclear. Here we show that an AHPND-causing strain of V. parahaemolyticus contains a 70-kbp plasmid (pVA1) with a postsegregational killing system, and that the ability to cause disease is abolished by the natural absence or experimental deletion of the plasmid-encoded homologs of the Photorhabdus insect-related (Pir) toxins PirA and PirB. We determined the crystal structure of the V. parahaemolyticus PirA and PirB (PirA(vp) and PirB(vp)) proteins and found that the overall structural topology of PirA(vp)/PirB(vp) is very similar to that of the Bacillus Cry insecticidal toxin-like proteins, despite the low sequence identity (<10%). This structural similarity suggests that the putative PirAB(vp) heterodimer might emulate the functional domains of the Cry protein, and in particular its pore-forming activity. The gene organization of pVA1 further suggested that pirAB(vp) may be lost or acquired by horizontal gene transfer via transposition or homologous recombination.


    Organizational Affiliation

    Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan; Department of Life Science, National Taiwan University, Taipei 104, Taiwan; Center of Bioscience and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan gracelow@mail.ncku.edu.tw h061453@mail.ncku.edu.tw wanghc@tmu.edu.tw.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinA, B446Vibrio parahaemolyticus M0605Mutation(s): 0 
Gene Names: AJ90_20625pirB
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.897α = 90
b = 128.618β = 90
c = 117.104γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
SHELXSphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description