8B4E

ToxR bacterial transcriptional regulator bound to 25 bp toxT promoter DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

ToxR activates the Vibrio cholerae virulence genes by tethering DNA to the membrane through versatile binding to multiple sites.

Canals, A.Pieretti, S.Muriel-Masanes, M.El Yaman, N.Plecha, S.C.Thomson, J.J.Fabrega-Ferrer, M.Perez-Luque, R.Krukonis, E.S.Coll, M.

(2023) Proc Natl Acad Sci U S A 120: e2304378120-e2304378120

  • DOI: https://doi.org/10.1073/pnas.2304378120
  • Primary Citation of Related Structures:  
    8B4B, 8B4C, 8B4D, 8B4E

  • PubMed Abstract: 

    ToxR, a Vibrio cholerae transmembrane one-component signal transduction factor, lies within a regulatory cascade that results in the expression of ToxT, toxin coregulated pilus, and cholera toxin. While ToxR has been extensively studied for its ability to activate or repress various genes in V. cholerae , here we present the crystal structures of the ToxR cytoplasmic domain bound to DNA at the toxT and ompU promoters. The structures confirm some predicted interactions, yet reveal other unexpected promoter interactions with implications for other potential regulatory roles for ToxR. We show that ToxR is a versatile virulence regulator that recognizes diverse and extensive, eukaryotic-like regulatory DNA sequences, that relies more on DNA structural elements than specific sequences for binding. Using this topological DNA recognition mechanism, ToxR can bind both in tandem and in a twofold inverted-repeat-driven manner. Its regulatory action is based on coordinated multiple binding to promoter regions near the transcription start site, which can remove the repressing H-NS proteins and prepares the DNA for optimal interaction with the RNA polymerase.


  • Organizational Affiliation

    Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cholera toxin transcriptional activator
A, B
109Vibrio choleraeMutation(s): 0 
Gene Names: toxRVC_0984
UniProt
Find proteins for P15795 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore P15795 
Go to UniProtKB:  P15795
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15795
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (25-MER)C [auth L]25Vibrio cholerae
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (25-MER)D [auth M]25Vibrio cholerae
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.669α = 90
b = 162.366β = 90
c = 86.628γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainBFU2014-53550-P
Spanish Ministry of Science, Innovation, and UniversitiesSpainBFU2017-83720-P
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2020-120141GB- I00
Spanish Ministry of Science, Innovation, and UniversitiesSpainMDM-2014-0435

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-09
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection