Structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA

Nature. 2002 Jun 27;417(6892):971-4. doi: 10.1038/nature00833.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism*
  • Binding Sites
  • Crystallography, X-Ray
  • DNA, Bacterial / genetics
  • DNA, Bacterial / metabolism*
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism
  • Dimerization
  • Helix-Turn-Helix Motifs
  • Homoserine / analogs & derivatives*
  • Homoserine / metabolism
  • Hydrogen Bonding
  • Hydrophobic and Hydrophilic Interactions
  • Models, Molecular
  • Molecular Sequence Data
  • Pheromones / metabolism*
  • Protein Structure, Quaternary
  • Protein Structure, Tertiary
  • Rhizobium / chemistry*
  • Transcription Factors / chemistry*
  • Transcription Factors / metabolism*


  • Bacterial Proteins
  • DNA, Bacterial
  • DNA-Binding Proteins
  • Pheromones
  • TraR protein, Agrobacterium tumefaciens
  • Transcription Factors
  • N-(beta-oxooctan-1-oyl)homoserine lactone
  • Homoserine

Associated data

  • PDB/1L3L