7R5A

Vibrio cholera ParD2:ParE2 antitoxin:toxin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.268 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Toxin:antitoxin ratio sensing autoregulation of the Vibrio cholerae parDE2 module.

Garcia-Rodriguez, G.Girardin, Y.Kumar Singh, R.Volkov, A.N.Van Dyck, J.Muruganandam, G.Sobott, F.Charlier, D.Loris, R.

(2024) Sci Adv 10: eadj2403-eadj2403

  • DOI: https://doi.org/10.1126/sciadv.adj2403
  • Primary Citation of Related Structures:  
    7R5A

  • PubMed Abstract: 

    The parDE family of toxin-antitoxin (TA) operons is ubiquitous in bacterial genomes and, in Vibrio cholerae , is an essential component to maintain the presence of chromosome II. Here, we show that transcription of the V. cholerae parDE2 (Vc parDE ) operon is regulated in a toxin:antitoxin ratio-dependent manner using a molecular mechanism distinct from other type II TA systems. The repressor of the operon is identified as an assembly with a 6:2 stoichiometry with three interacting ParD2 dimers bridged by two ParE2 monomers. This assembly docks to a three-site operator containing 5'- GGTA-3' motifs. Saturation of this TA complex with ParE2 toxin results in disruption of the interface between ParD2 dimers and the formation of a TA complex of 2:2 stoichiometry. The latter is operator binding-incompetent as it is incompatible with the required spacing of the ParD2 dimers on the operator.


  • Organizational Affiliation

    Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin105Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: VC_A0359
UniProt
Find proteins for Q9KMJ0 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KMJ0 
Go to UniProtKB:  Q9KMJ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KMJ0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Antitoxin ParD
B, C, D
80Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: parDVC_A0360.1
UniProt
Find proteins for P58093 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore P58093 
Go to UniProtKB:  P58093
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58093
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.268 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.78α = 90
b = 65.78β = 90
c = 127.44γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-27
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-01-31
    Changes: Database references