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 

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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 formation, production of antimicrobials, DNA exchange, pathogenesis and symbiosis ...

    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

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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional activator protein traRE [auth A],
F [auth B],
G [auth C],
H [auth D]		234Agrobacterium tumefaciensMutation(s): 6 
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: 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'A [auth E],
B [auth F],
C [auth G],
D [auth H]		20N/A
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		E [auth A],
F [auth B],
G [auth C],
H [auth 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
b = 58.37β = 102.81
c = 127.453γ = 90
Software Package:
Software NamePurpose
CNSrefinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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