9HVJ

Ligand binding domain of Roseburia intestinalis L1-82 uracil chemoreceptor (dCache) in complex with uracil and acetate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 
    0.189 (Depositor), 0.187 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted URAClick on this verticalbar to view detailsBest fitted ACTClick on this verticalbar to view details

This is version 1.0 of the entry. See complete history


Literature

Specificities of Chemosensory Receptors in the Human Gut Microbiota.

Xu, W.Jalomo-Khayrova, E.Gumerov, V.M.Ross, P.A.Kobel, T.S.Schindler, D.Bange, G.Zhulin, I.B.Sourjik, V.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.02.11.637667
  • Primary Citation of Related Structures:  
    9HVJ

  • PubMed Abstract: 

    The human gut is rich in metabolites and harbors a complex microbial community, yet the sensory repertoire of its commensal bacteria remains largely uncharacterized. Here we systematically mapped ligand specificities of extracytoplasmic sensory domains from twenty members of the human gut microbiota, with a primary focus on the abundant and physiologically important class of Clostridia. We identified diverse metabolites as specific stimuli for three major functional classes of transmembrane receptors. We further characterized novel subsets of sensors belonging to the Cache superfamily, specific for lactate, dicarboxylic acids, and for uracil and short-chain fatty acids (SCFAs), respectively, and investigated the evolution of their ligand specificity. Structural and biochemical analysis of the newly described dCache_1UR domain revealed an independent binding of uracil and SCFA at distinct modules. Altogether, we could identify or predict specificities for over a half of the Cache-type chemotactic sensors in the selected gut commensals, with the carboxylic acids representing the largest class of ligands. Among those, the most commonly found specificities were for lactate and formate, indicating particular importance of these metabolites in the human gut microbiome and consistent with their observed beneficial impact on the growth of selected bacterial species.


  • Organizational Affiliation

    Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cache domain protein301Roseburia intestinalis L1-82Mutation(s): 0 
Gene Names: mcpC_1RIL182_00127ROSINTL182_06964
UniProt
Find proteins for C7GAN4 (Roseburia intestinalis L1-82)
Explore C7GAN4 
Go to UniProtKB:  C7GAN4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7GAN4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free:  0.189 (Depositor), 0.187 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35α = 90
b = 93.08β = 92.19
c = 44.38γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted URAClick on this verticalbar to view detailsBest fitted ACTClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany464366151

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release