8GUG

Structure of VPA0770 toxin bound to VPA0769 antitoxin in Vibrio parahaemolyticus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural insights of the toxin-antitoxin system VPA0770-VPA0769 in Vibrio parahaemolyticus.

Zhang, Y.Song, X.Chen, C.Liu, L.Xu, Y.Zhang, N.Huang, W.Zheng, J.Yuan, W.Tang, L.Lin, Z.

(2023) Int J Biol Macromol 242: 124755-124755

  • DOI: https://doi.org/10.1016/j.ijbiomac.2023.124755
  • Primary Citation of Related Structures:  
    8GUG

  • PubMed Abstract: 

    Toxin-antitoxin (TA) systems are involved in both normal bacterial physiology and pathogenicity, including gene regulation, antibiotic resistance, and bacteria persistence under stressful environments. In pathogenic Vibrio parahaemolyticus, however, TA interaction and assembly remain largely unknown. In this work, we identified a new RES-Xre type II TA module, encoded by gene cluster vpa0770-vpa0769 on chromosome II of V. parahaemolyticus. Ectopic expression of the VPA0770 toxin rapidly arrests the growth of E. coli cells, which can be neutralized by co-expression of the VPA0769 antitoxin. To decipher the action mechanism, we determined the crystal structure of the VPA0770-VPA0769 TA complex. VPA0770 and VPA0769 proteins can assemble into two types of large complexes, a W-shaped hetero-hexamer and a donut-like hetero-dodecamer, in a concentration-dependent manner in solution. Disruption of the TA interface results in a loss of the antitoxic phenotype. The toxicity of the VPA0770 toxin, which harbors a NAD + -binding pocket, may be largely ascribed to its highly effective capability to degrade intracellular NAD + . Our study provides a structural basis for a better understanding of diverse molecular mechanisms employed by human pathogens.


  • Organizational Affiliation

    School of Life Sciences, Tianjin University, Tianjin 300073, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RES domain-containing protein156Vibrio parahaemolyticus RIMD 2210633Mutation(s): 1 
Gene Names: VPA0770
UniProt
Find proteins for Q87I36 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633))
Explore Q87I36 
Go to UniProtKB:  Q87I36
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ87I36
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DUF2384 domain-containing protein
B, C
150Vibrio parahaemolyticus RIMD 2210633Mutation(s): 0 
Gene Names: VPA0769
UniProt
Find proteins for Q87I37 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633))
Explore Q87I37 
Go to UniProtKB:  Q87I37
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ87I37
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.915α = 90
b = 104.725β = 90
c = 116.218γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
PHENIXphasing
HKL-3000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21974093

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release