5JUF | pdb_00005juf

Crystal structure of the apo form of ComR from S. thermophilus.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.216 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5JUF

This is version 1.3 of the entry. See complete history

Literature

Structural Insights into Streptococcal Competence Regulation by the Cell-to-Cell Communication System ComRS.

Talagas, A.Fontaine, L.Ledesma-Garca, L.Mignolet, J.Li de la Sierra-Gallay, I.Lazar, N.Aumont-Nicaise, M.Federle, M.J.Prehna, G.Hols, P.Nessler, S.

(2016) PLoS Pathog 12: e1005980-e1005980

  • DOI: https://doi.org/10.1371/journal.ppat.1005980
  • Primary Citation Related Structures: 
    5JUB, 5JUF

  • PubMed Abstract: 

    In Gram-positive bacteria, cell-to-cell communication mainly relies on extracellular signaling peptides, which elicit a response either indirectly, by triggering a two-component phosphorelay, or directly, by binding to cytoplasmic effectors. The latter comprise the RNPP family (Rgg and original regulators Rap, NprR, PrgX and PlcR), whose members regulate important bacterial processes such as sporulation, conjugation, and virulence. RNPP proteins are increasingly considered as interesting targets for the development of new antibacterial agents. These proteins are characterized by a TPR-type peptide-binding domain, and except for Rap proteins, also contain an N-terminal HTH-type DNA-binding domain and display a transcriptional activity. Here, we elucidate the structure-function relationship of the transcription factor ComR, a new member of the RNPP family, which positively controls competence for natural DNA transformation in streptococci. ComR is directly activated by the binding of its associated pheromone XIP, the mature form of the comX/sigX-inducing-peptide ComS. The crystal structure analysis of ComR from Streptococcus thermophilus combined with a mutational analysis and in vivo assays allows us to propose an original molecular mechanism of the ComR regulation mode. XIP-binding induces release of the sequestered HTH domain and ComR dimerization to allow DNA binding. Importantly, we bring evidence that this activation mechanism is conserved and specific to ComR orthologues, demonstrating that ComR is not an Rgg protein as initially proposed, but instead constitutes a new member of the RNPP family. In addition, identification of XIP and ComR residues important for competence activation constitutes a crucial step towards the design of antagonistic strategies to control gene exchanges among streptococci.


  • Organizational Affiliation
    • Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France.

Macromolecule Content 

  • Total Structure Weight: 36.93 kDa 
  • Atom Count: 2,625 
  • Modeled Residue Count: 299 
  • Deposited Residue Count: 310 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcriptional regulator310Streptococcus thermophilus LMD-9Mutation(s): 0 
Gene Names: BN551_00358
UniProt
Find proteins for A0A1L1QK15 (Streptococcus thermophilus (strain ATCC BAA-491 / LMD-9))
Explore A0A1L1QK15 
Go to UniProtKB:  A0A1L1QK15
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1L1QK15
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.216 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.82α = 90
b = 141.68β = 90
c = 78.55γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
CRANK2phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-12-14
    Changes: Database references
  • Version 1.2: 2025-04-09
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2025-10-01
    Changes: Advisory, Derived calculations