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 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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


  • 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.,Sect.D 58: 1362


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRANSCRIPTIONAL ACTIVATOR PROTEIN TRAR
A, B, C, D
234Rhizobium radiobacterGene Names: traR
Find proteins for P33905 (Rhizobium radiobacter)
Go to UniProtKB:  P33905
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP *CP*TP*GP*CP*AP*CP*AP*T)-3'E,F,G,H18N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OOA
Query on OOA

Download SDF File 
Download CCD File 
A, B, C, D
3-OXOOCTANOIC ACID
C8 H14 O3
FWNRRWJFOZIGQZ-UHFFFAOYSA-N
 Ligand Interaction
HSL
Query on HSL

Download SDF File 
Download CCD File 
A, B, C, D
HOMOSERINE LACTONE
C4 H7 N O2
QJPWUUJVYOJNMH-VKHMYHEASA-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 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 = 90.00
b = 94.678β = 90.00
c = 209.669γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
SnBphasing
SCALAdata scaling
MOSFLMdata reduction
CNXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-08-29
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-07-05
    Type: Refinement description