Vc1313-LBD bound to D-lysine

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

Starting Model: other
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Ligand Structure Quality Assessment 

This is version 1.5 of the entry. See complete history


D-amino acids signal a stress-dependent run-away response in Vibrio cholerae.

Irazoki, O.Ter Beek, J.Alvarez, L.Mateus, A.Colin, R.Typas, A.Savitski, M.M.Sourjik, V.Berntsson, R.P.Cava, F.

(2023) Nat Microbiol 8: 1549-1560

  • DOI: https://doi.org/10.1038/s41564-023-01419-6
  • Primary Citation of Related Structures:  
    8BSA, 8BSB

  • PubMed Abstract: 

    To explore favourable niches while avoiding threats, many bacteria use a chemotaxis navigation system. Despite decades of studies on chemotaxis, most signals and sensory proteins are still unknown. Many bacterial species release D-amino acids to the environment; however, their function remains largely unrecognized. Here we reveal that D-arginine and D-lysine are chemotactic repellent signals for the cholera pathogen Vibrio cholerae. These D-amino acids are sensed by a single chemoreceptor MCP DRK co-transcribed with the racemase enzyme that synthesizes them under the control of the stress-response sigma factor RpoS. Structural characterization of this chemoreceptor bound to either D-arginine or D-lysine allowed us to pinpoint the residues defining its specificity. Interestingly, the specificity for these D-amino acids appears to be restricted to those MCP DRK orthologues transcriptionally linked to the racemase. Our results suggest that D-amino acids can shape the biodiversity and structure of complex microbial communities under adverse conditions.

  • Organizational Affiliation

    The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methyl-accepting chemotaxis protein
A, B
177Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: FLM12_13895
Find proteins for Q9KSE4 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KSE4 
Go to UniProtKB:  Q9KSE4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KSE4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.337α = 75.32
b = 44.927β = 79.17
c = 56.939γ = 73.69
Software Package:
Software NamePurpose
Cootmodel building
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2016-03599
Knut and Alice Wallenberg FoundationSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2023-06-28
    Changes: Database references
  • Version 1.2: 2023-07-05
    Changes: Database references
  • Version 1.3: 2023-08-09
    Changes: Database references
  • Version 1.4: 2023-11-15
    Changes: Data collection, Source and taxonomy
  • Version 1.5: 2024-05-01
    Changes: Refinement description