Deciphering the action of aromatic effectors on the prokaryotic enhancer-binding protein XylR: a structural model of its N-terminal domain

Environ Microbiol. 2002 Jan;4(1):29-41. doi: 10.1046/j.1462-2920.2002.00265.x.


The prokaryotic enhancer-binding protein XylR is the central regulator of the toluene degradation pathway in Pseudomonas species. Copious genetic and biochemical data indicate that the N-terminal domain of the protein (domain A) interacts directly with m-xylene, which renders the protein competent as a transcriptional activator. Single-site and shuffling mutants of XylR or homologues have been reported to change or expand their effector profiles. Here, we follow a fold recognition approach to generate three-dimensional models of the domain A of XylR and DmpR with the purpose of deciphering the molecular activity of this protein family. The model is based on the crystallographic data of the rat catechol O-methyltransferase, a typical alpha/beta fold, consisting of eight alpha-helices and seven beta-strands. The fold identification is supported by physico-chemical properties of conserved amino acids, distribution of residues characteristic of the sequence families and confrontation with experimental data. The model not only provides a rationale for understanding published experimental data, but also suggests the molecular mechanism of the activation step and is a potentially useful conceptual tool for designing regulators with predefined inducer specificities.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Bacterial Proteins / chemistry*
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Structure, Secondary
  • Pseudomonas / chemistry
  • Pseudomonas / metabolism
  • Rats
  • Sequence Alignment
  • Structure-Activity Relationship
  • Toluene / metabolism
  • Trans-Activators / chemistry*
  • Transcription Factors / chemistry*
  • Transcription Factors / metabolism
  • Xylenes / metabolism


  • Bacterial Proteins
  • DNA-Binding Proteins
  • DmpR protein, Pseudomonas
  • Trans-Activators
  • Transcription Factors
  • XylR protein, Pseudomonas
  • Xylenes
  • Toluene
  • 3-xylene