6DSP | pdb_00006dsp

LsrB from Clostridium saccharobutylicum in complex with AI-2

• PDB DOI: https://doi.org/10.2210/pdb6DSP/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Clostridium saccharobutylicum DSM 13864
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-06-14 Released: 2019-02-06 
• Deposition Author(s): Torcato, I.M., Xavier, K.B., Miller, S.T.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 
  0.177 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.160 (DCC) 

Starting Model: experimental

Literature

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 Biological Chem 294: 4450-4463

• PubMed: 30696769 
• DOI: https://doi.org/10.1074/jbc.RA118.006938
• Primary Citation Related Structures: 
  6DSP


• 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.

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Organizational Affiliation: 
• From the Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal.
the Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal.
the Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, and.
the Chronic Disease Research Center (CEDOC), NOVA Medical School, Universidade NOVA de Lisboa, Rua Câmara Pestana, 6, 1150-082 Lisboa, Portugal.
the Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, and [e-mail].
From the Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal, [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 75.06 kDa 
• Atom Count: 5,327 
• Modeled Residue Count: 652 
• Deposited Residue Count: 694 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Autoinducer 2-binding protein LsrB	A, B	347	Clostridium saccharobutylicum DSM 13864	Mutation(s): 0  Gene Names: lsrB, CLSA_c21430
UniProt
Find proteins for U5MRH9 (Clostridium saccharobutylicum DSM 13864) Explore U5MRH9  Go to UniProtKB:  U5MRH9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PAV	C [auth A], D [auth B]	(2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran C5 H10 O5 BVIYGXUQVXBHQS-IUYQGCFVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free:  0.177 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.160 (DCC) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.78	α = 90
b = 90.78	β = 90
c = 182.81	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Torcato, I.M., Xavier, K.B., Miller, S.T.

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Funding Organization	Location	Grant Number
Other government	Portugal	PTDC/BIA-MIC/4188/14

Revision History  

• 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