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

Abstract

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.

Domain Architectures of σ54-Dependent Transcriptional Activators

“…Genetic and biochemical data indicate that the N-terminal domain of the protein interacts directly with m-xylene, which renders the protein competent as a transcriptional activator. Three-dimensional models that go some way to explaining the molecular basis for interaction with substrate have been generated for the V4R domains of XylR and DmpR (17).…”

Characterisation of the Putative Effector Interaction Site of the Regulatory HbpR Protein from Pseudomonas azelaica by Site-Directed Mutagenesis

“…Attempts to obtain direct structural information on the proteins of this subclass have been frustrated by the difficulty to purify and stabilize the full protein. Nevertheless, a structural model for the XylR A-domain was proposed based on low but pertinent similarity to the A-chain of eukaryotic catechol O-methyl transferase [22]. This model, however, consists of only a single XylR A-domain protomer whereas the current hypothesis predicts that proteins from this class undergo an activation cycle of multimerization and multimer disassembly [23].…”

“…HbpR domains are depicted to scale according to the predictions by Jaspers et al [7]. (B) to (E) Fitting used swiss - model and was performed on XylR A-domain PDB coordinates as calculated by Devos et al [22]. (B) Ribbon model of HbpR A-domain residues 11–209, with predicted coils, alpha-helices and beta-sheets indicated.…”

Linking genes to microbial growth kinetics—An integrated biochemical systems engineering approach

“…The multimerized protein undergoes conformational changes producing a transcriptionally competent form of XylR (XylR a ) (Devos et al, 2002), which results in rapid transition between the active and inactive forms of the protein (Shingler, 2003). Comparing the expression used for Pr to the one presented in our previous work with the Pr/Ps system (Koutinas et al, 2010), the following minor differences can be identified.…”