LsrB from Clostridium saccharobutylicum in complex with AI-2

Experimental Data Snapshot

  • Resolution: 1.37 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.159 

Starting Model: experimental
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Identification of novel autoinducer-2 receptors inClostridiareveals plasticity in the binding site of the LsrB receptor family.

Torcato, I.M.Kasal, M.R.Brito, P.H.Miller, S.T.Xavier, K.B.

(2019) J Biol Chem 294: 4450-4463

  • DOI: https://doi.org/10.1074/jbc.RA118.006938
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Autoinducer-2 (AI-2) is unique among quorum-sensing signaling molecules, as it is produced and recognized by a wide variety of bacteria and thus facilitates interspecies communication. To date, two classes of AI-2 receptors have been identified: the LuxP-type, present in the Vibrionales , and the LsrB-type, found in a number of phylogenetically distinct bacterial families. Recently, AI-2 was shown to affect the colonization levels of a variety of bacteria in the microbiome of the mouse gut, including members of the genus Clostridium , but no AI-2 receptor had been identified in this genus. Here, we identify a noncanonical, functional LsrB-type receptor in Clostridium saccharobutylicum. This novel LsrB-like receptor is the first one reported with variations in the binding-site amino acid residues that interact with AI-2. The crystal structure of the C. saccharobutylicum receptor determined at 1.35 Å resolution revealed that it binds the same form of AI-2 as the other known LsrB-type receptors, and isothermal titration calorimetry (ITC) assays showed that binding of AI-2 occurs at a submicromolar concentration. Using phylogenetic analysis, we inferred that the newly identified noncanonical LsrB receptor shares a common ancestor with known LsrB receptors and that noncanonical receptors are present in bacteria from different phyla. This led us to identify putative AI-2 receptors in bacterial species in which no receptors were known, as in bacteria belonging to the Spirochaetes and Actinobacteria phyla. Thus, this work represents a significant step toward understanding how AI-2-mediated quorum sensing influences bacterial interactions in complex biological niches.

  • Organizational Affiliation

    From the Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Autoinducer 2-binding protein LsrB
A, B
347Clostridium saccharobutylicum DSM 13864Mutation(s): 0 
Gene Names: lsrBCLSA_c21430
Find proteins for U5MRH9 (Clostridium saccharobutylicum DSM 13864)
Explore U5MRH9 
Go to UniProtKB:  U5MRH9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU5MRH9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PAV

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C5 H10 O5
Experimental Data & Validation

Experimental Data

  • Resolution: 1.37 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.159 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.78α = 90
b = 90.78β = 90
c = 182.81γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other governmentPortugalPTDC/BIA-MIC/4188/14

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2019-08-21
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Derived calculations, Structure summary
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description