2Q0O

Crystal structure of an anti-activation complex in bacterial quorum sensing


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for antiactivation in bacterial quorum sensing.

Chen, G.Jeffrey, P.D.Fuqua, C.Shi, Y.Chen, L.

(2007) Proc.Natl.Acad.Sci.Usa 104: 16474-16479

  • DOI: 10.1073/pnas.0704843104

  • PubMed Abstract: 
  • Bacteria can communicate via diffusible signal molecules they generate and release to coordinate their behavior in response to the environment. Signal molecule concentration is often proportional to bacterial population density, and when this reaches ...

    Bacteria can communicate via diffusible signal molecules they generate and release to coordinate their behavior in response to the environment. Signal molecule concentration is often proportional to bacterial population density, and when this reaches a critical concentration, reflecting a bacterial quorum, specific behaviors including virulence, symbiosis, and horizontal gene transfer are activated. Quorum-sensing regulation in many Gram-negative bacteria involves acylated homoserine lactone signals that are perceived through binding to LuxR-type, acylated-homoserine-lactone-responsive transcription factors. Bacteria of the rhizobial group employ the LuxR-type transcriptional activator TraR in quorum sensing, and its activity is further regulated through interactions with the TraM antiactivator. In this study, we have crystallographically determined the 3D structure of the TraR-TraM antiactivation complex from Rhizobium sp. strain NGR234. Unexpectedly, the antiactivator TraM binds to TraR at a site distinct from its DNA-binding motif and induces an allosteric conformational change in the protein, thereby preventing DNA binding. Structural analysis reveals a highly conserved TraR-TraM interface and suggests a mechanism for antiactivation complex formation. This structure may inform alternative strategies to control quorum-sensing-regulated microbial activity including amelioration of infectious disease and antibiotic resistance. In addition, the structural basis of antiactivation presents a regulatory interaction that provides general insights relevant to the field of transcription regulation and signal transduction.


    Organizational Affiliation

    Department of Biology, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable transcriptional activator protein traR
A, B
236Sinorhizobium fredii (strain NBRC 101917 / NGR234)Mutation(s): 0 
Gene Names: traR
Find proteins for P55407 (Sinorhizobium fredii (strain NBRC 101917 / NGR234))
Go to UniProtKB:  P55407
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Probable transcriptional repressor traM
C, D
107Sinorhizobium fredii (strain NBRC 101917 / NGR234)Mutation(s): 0 
Gene Names: traM
Find proteins for P55408 (Sinorhizobium fredii (strain NBRC 101917 / NGR234))
Go to UniProtKB:  P55408
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LAE
Query on LAE

Download SDF File 
Download CCD File 
A, B
3-OXO-OCTANOIC ACID (2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE
N-(3-OXO-OCTANAL-1-YL)-HOMOSERINE LACTONE
C12 H19 N O4
FXCMGCFNLNFLSH-JTQLQIEISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.235 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 56.900α = 94.87
b = 62.480β = 110.45
c = 65.500γ = 99.17
Software Package:
Software NamePurpose
d*TREKdata scaling
CrystalCleardata collection
PHASERphasing
CNSrefinement
d*TREKdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-09-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance