1L3L

Crystal structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA.

Zhang, R.G., Pappas, T., Brace, J.L., Miller, P.C., Oulmassov, T., Molyneaux, J.M., Anderson, J.C., Bashkin, J.K., Winans, S.C., Joachimiak, A.

(2002) Nature 417: 971-974

  • DOI: 10.1038/nature00833

  • PubMed Abstract: 

    • Many proteobacteria are able to monitor their population densities through the release of pheromones known as N-acylhomoserine lactones. At high population densities, these pheromones elicit diverse responses that include bioluminescence, biofilm for ...

    Many proteobacteria are able to monitor their population densities through the release of pheromones known as N-acylhomoserine lactones. At high population densities, these pheromones elicit diverse responses that include bioluminescence, biofilm formation, production of antimicrobials, DNA exchange, pathogenesis and symbiosis. Many of these regulatory systems require a pheromone-dependent transcription factor similar to the LuxR protein of Vibrio fischeri. Here we present the structure of a LuxR-type protein. TraR of Agrobacterium tumefaciens was solved at 1.66 A as a complex with the pheromone N-3-oxooctanoyl-L-homoserine lactone (OOHL) and its TraR DNA-binding site. The amino-terminal domain of TraR is an alpha/beta/alpha sandwich that binds OOHL, whereas the carboxy-terminal domain contains a helix turn helix DNA-binding motif. The TraR dimer displays a two-fold symmetry axis in each domain; however, these two axes of symmetry are at an approximately 90 degree angle, resulting in a pronounced overall asymmetry of the complex. The pheromone lies fully embedded within the protein with virtually no solvent contact, and makes numerous hydrophobic contacts with the protein as well as four hydrogen bonds: three direct and one water-mediated.

    Organizational Affiliation: 

    Bioscience Division/Structural Biology Center, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, Illinois 60439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Transcriptional activator protein traR
A, B, C, D
234Rhizobium radiobacterMutation(s): 0 
Gene Names: traR
Find proteins for P33905 (Rhizobium radiobacter)
Go to UniProtKB:  P33905
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP*CP*TP*GP*CP*AP*CP*AP*TP*C)-3'E,F,G,H20N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LAE
Query on LAE
Download SDF File 
Download CCD File 
A, B, C, D
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.246 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 92.298α = 90.00
b = 58.370β = 102.81
c = 127.453γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
d*TREKdata reduction
CNSphasing
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-07-03
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description