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 

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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: https://doi.org/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 the tumour- inducing plasmid, responsible for plant crown gall disease ...

    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

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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional activator protein TraR
A, B, C, D
234Agrobacterium tumefaciensMutation(s): 0 
Gene Names: traR
UniProt
Find proteins for P33905 (Rhizobium radiobacter)
Explore P33905 
Go to UniProtKB:  P33905
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33905
Protein Feature View
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  • Reference Sequence

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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, H
18synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LAE
Query on LAE
Download Ideal Coordinates CCD File 
I [auth A],
J [auth B],
K [auth C],
L [auth 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, D
L-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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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