1H0M

Three-dimensional structure of the quorum sensing protein TraR bound to its autoinducer and to its target DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.233 

wwPDB Validation   3D Report Full Report



Literature

The Crystal Structure of the Quorum Sensing Protein Trar Bound to its Autoinducer and Target DNA

Vannini, A.Volpari, C.Gargioli, C.Muraglia, E.Cortese, R.De Francesco, R.Neddermann, P.Di Marco, S.

(2002) EMBO J 21: 4393

  • DOI: 10.1093/emboj/cdf459
  • Primary Citation of Related Structures:  
    1H0M

  • PubMed Abstract: 
  • The quorum sensing system allows bacteria to sense their cell density and initiate an altered pattern of gene expression after a sufficient quorum of cells has accumulated. In Agrobacterium tumefaciens, quorum sensing controls conjugal transfer of th ...

    The quorum sensing system allows bacteria to sense their cell density and initiate an altered pattern of gene expression after a sufficient quorum of cells has accumulated. In Agrobacterium tumefaciens, quorum sensing controls conjugal transfer of the tumour- inducing plasmid, responsible for plant crown gall disease. The core components of this system are the transcriptional regulator TraR and its inducing ligand N-(3-oxo-octanoyl)-L-homoserine lactone. This complex binds DNA and activates gene expression. We have determined the crystal structure of TraR in complex with its autoinducer and target DNA (PDB code 1h0m). The protein is dimeric, with each monomer composed of an N-terminal domain, which binds the ligand in an enclosed cavity far from the dimerization region, and a C-terminal domain, which binds DNA via a helix-turn-helix motif. The structure reveals an asymmetric homodimer, with one monomer longer than the other. The N-terminal domain resembles GAF/PAS domains, normally fused to catalytic signalling domains. In TraR, the gene fusion is between a GAF/PAS domain and a DNA-binding domain, resulting in a specific transcriptional regulator involved in quorum sensing.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Diffraction Studies of the Transcriptional Regulator Trar Bound to its Cofactor and to a Specific DNA Sequence
      Vannini, A., Volpari, C., Gargioli, C., Muraglia, E., De Francesco, R., Neddermann, P., Di Marco, S.
      (2002) Acta Crystallogr D Biol Crystallogr 58: 1362

    Organizational Affiliation

    IRBM P. Angeletti, Via Pontina Km 30.600, I-00040 Pomezia, Rome, Italy.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional activator protein TraRABCD234Agrobacterium tumefaciensMutation(s): 0 
Gene Names: traR
Find proteins for P33905 (Rhizobium radiobacter)
Explore P33905 
Go to UniProtKB:  P33905
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP *CP*TP*GP*CP*AP*CP*AP*T)-3'E, F, G, H18synthetic construct
    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: 3.00 Å
    • R-Value Free: 0.285 
    • R-Value Work: 0.233 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 66.993α = 90
    b = 94.678β = 90
    c = 209.669γ = 90
    Software Package:
    Software NamePurpose
    MOSFLMdata reduction
    SCALAdata scaling
    SnBphasing
    SHARPphasing
    CNXrefinement

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2002-08-29
      Type: Initial release
    • Version 1.1: 2011-05-08
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2017-07-05
      Changes: Refinement description
    • Version 2.0: 2020-12-16
      Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary