the competence regulator ComR from Streptococcus vestibularis in complex with its cognate signaling peptide XIP

Experimental Data Snapshot

  • Resolution: 3.39 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.248 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Molecular dissection of pheromone selectivity in the competence signaling system ComRS of streptococci.

Ledesma-Garcia, L.Thuillier, J.Guzman-Espinola, A.Ensinck, I.Li de la Sierra-Gallay, I.Lazar, N.Aumont-Nicaise, M.Mignolet, J.Soumillion, P.Nessler, S.Hols, P.

(2020) Proc Natl Acad Sci U S A 117: 7745-7754

  • DOI: https://doi.org/10.1073/pnas.1916085117
  • Primary Citation of Related Structures:  
    6HU8, 6HUA, 6QER

  • PubMed Abstract: 

    Competence allows bacteria to internalize exogenous DNA fragments for the acquisition of new phenotypes such as antibiotic resistance or virulence traits. In most streptococci, competence is regulated by ComRS signaling, a system based on the mature ComS pheromone (XIP), which is internalized to activate the (R)RNPP-type ComR sensor by triggering dimerization and DNA binding. Cross-talk analyses demonstrated major differences of selectivity between ComRS systems and raised questions concerning the mechanism of pheromone-sensor recognition and coevolution. Here, we decipher the molecular determinants of selectivity of the closely related ComRS systems from Streptococcus thermophilus and Streptococcus vestibularis Despite high similarity, we show that the divergence in ComR-XIP interaction does not allow reciprocal activation. We perform the structural analysis of the ComRS system from S. vestibularis. Comparison with its ortholog from S. thermophilus reveals an activation mechanism based on a toggle switch involving the recruitment of a key loop by the XIP C terminus. Together with a broad mutational analysis, we identify essential residues directly involved in peptide binding. Notably, we generate a ComR mutant that displays a fully reversed selectivity toward the heterologous pheromone with only five point mutations, as well as other ComR variants featuring XIP bispecificity and/or neofunctionalization for hybrid XIP peptides. We also reveal that a single XIP mutation relaxes the strictness of ComR activation, suggesting fast adaptability of molecular communication phenotypes. Overall, this study is paving the way toward the rational design or directed evolution of artificial ComRS systems for a range of biotechnological and biomedical applications.

  • Organizational Affiliation

    Louvain Institute of Biomolecular Science and Technology, Biochemistry and Genetics of Microorganisms, Université catholique de Louvain, B-1348 Louvain-La-Neuve, Belgium.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B
310Streptococcus vestibularis F0396Mutation(s): 0 
Gene Names: HMPREF9192_0126
Find proteins for E3CNF6 (Streptococcus vestibularis F0396)
Explore E3CNF6 
Go to UniProtKB:  E3CNF6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE3CNF6
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
XIP signaling peptide
C, D
8Streptococcus vestibularis F0396Mutation(s): 0 
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.39 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.248 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.19α = 90
b = 84.03β = 90
c = 152.75γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2020-04-01
    Changes: Database references
  • Version 1.2: 2020-04-22
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description