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
  • Primary Citation of Related Structures:  
    1L3L

  • 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: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional activator protein traRA, B, C, D234Agrobacterium tumefaciensMutation(s): 6 
Gene Names: traR
Find proteins for P33905 (Rhizobium radiobacter)
Explore P33905 
Go to UniProtKB:  P33905
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    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 Ideal Coordinates CCD File 
    A, B, C, D
    		3-OXO-OCTANOIC ACID (2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE
    C12 H19 N O4
    FXCMGCFNLNFLSH-JTQLQIEISA-N    		 Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    MSE
    Query on MSE    		A,B,C,DL-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
    b = 58.37β = 102.81
    c = 127.453γ = 90
    Software Package:
    Software NamePurpose
    CNSrefinement
    d*TREKdata reduction
    HKL-2000data scaling
    CNSphasing

    Structure Validation

    View Full Validation Report


    View more in-depth experimental data

    Entry History 

    Deposition Data

    Revision History 

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