4NOO

Molecular mechanism for self-protection against type VI secretion system in Vibrio cholerae

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

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Literature

Molecular mechanism for self-protection against the type VI secretion system in Vibrio cholerae.

Yang, X., Xu, M., Wang, Y., Xia, P., Wang, S., Ye, B., Tong, L., Jiang, T., Fan, Z.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1094-1103

  • DOI: 10.1107/S1399004714001242
  • Primary Citation of Related Structures:  
    4NOO

  • PubMed Abstract: 

    • VgrG proteins form the spike of the type VI secretion system (T6SS) syringe-like complex. VgrG3 of Vibrio cholerae degrades the peptidoglycan cell wall of rival bacteria via its C-terminal region (VgrG3C) through its muramidase activity. VgrG3C consists of a peptidoglycan-binding domain (VgrG3C(PGB)) and a putative catalytic domain (VgrG3C(CD)), and its activity can be inhibited by its immunity protein partner TsiV3 ...

    VgrG proteins form the spike of the type VI secretion system (T6SS) syringe-like complex. VgrG3 of Vibrio cholerae degrades the peptidoglycan cell wall of rival bacteria via its C-terminal region (VgrG3C) through its muramidase activity. VgrG3C consists of a peptidoglycan-binding domain (VgrG3C(PGB)) and a putative catalytic domain (VgrG3C(CD)), and its activity can be inhibited by its immunity protein partner TsiV3. Here, the crystal structure of V. cholerae VgrG3C(CD) in complex with TsiV3 is presented at 2.3 Å resolution. VgrG3C(CD) adopts a chitosanase fold. A dimer of TsiV3 is bound in the deep active-site groove of VgrG3C(CD), occluding substrate binding and distorting the conformation of the catalytic dyad. Gln91 and Arg92 of TsiV3 are located in the centre of the interface and are important for recognition of VgrG3C. Mutation of these residues destabilized the complex and abolished the inhibitory activity of TsiV3 against VgrG3C toxicity in cells. Disruption of TsiV3 dimerization also weakened the complex and impaired the inhibitory activity. These structural, biochemical and functional data define the molecular mechanism underlying the self-protection of V. cholerae and expand the understanding of the role of T6SS in bacterial competition.

    Organizational Affiliation: 

    Chinese Academy of Sciences Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VgrG proteinA, C205Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: VC_A0123, vgrG3
EC: 3.2.1
UniProt
Find proteins for Q9KN42 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KN42 
Go to UniProtKB:  Q9KN42
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KN42
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Putative uncharacterized proteinB, D98Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: VC_A0124, tsiV3
UniProt
Find proteins for Q9KN41 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KN41 
Go to UniProtKB:  Q9KN41
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KN41
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A, C L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.502α = 90
b = 116.034β = 94.05
c = 68.225γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2014-04-16
    Changes: Database references