Crystal structure of an IclR homologue fromMicrobacteriumsp. strain HM58-2

Abstract

The bacterial transcription factor IclR (isocitrate lyase regulator) is a member of a one-component signal transduction system, which shares the common motif of a helix-turn-helix (HTH)-type DNA-binding domain (DBD) connected to a substrate-binding domain (SBD). Here, the crystal structure of an IclR homologue (Mi-IclR) from Microbacterium sp. strain HM58-2, which catabolizes acylhydrazide as the sole carbon source, is reported. Mi-IclR is expected to regulate an operon responsible for acylhydrazide degradation as an initial step. Native single-wavelength anomalous diffraction (SAD) experiments were performed in combination with molecular replacement. CRANK2 from the CCP4 suite successfully phased and modelled the complete structure of a homotetramer composed of 1000 residues in an asymmetric unit, and the model was refined to 2.1 Å resolution. The overall structure of Mi-IclR shared the same domain combination as other known IclR structures, but the relative geometry between the DBD and SBD differs. Accordingly, the geometry of the Mi-IclR tetramer was unique: the putative substrate-binding site in each subunit is accessible from the outside of the tetramer, as opposed to buried inside as in the previously known IclR structures. These differences in the domain geometry may contribute to the transcriptional regulation of IclRs.

Functional and Structural Characterization of an IclR Family Transcription Factor for the Development of Dicarboxylic Acid Biosensors

“…Analysis of structurally characterized members of the IclR family suggested that deviations from this fold across this family are limited to amino acid sidechain positions within the binding pocket and to perturbations of the loop that is part of the binding pocket [9]. While the IclR family members appear to share the common architecture of DBD and LBD, variations in the relative orientation of the DBDs and LBDs is indicative of the flexibility of the linker connecting these domains and may contribute to the variety of functions and mechanisms demonstrated by IclR family representatives [10].…”

Functional and structural characterization of an IclR family transcription factor for the development of dicarboxylic acid biosensors

“…Structural characterization of IclR members suggested that deviations from this fold are limited to amino acid sidechain positions within the binding pocket and to perturbations of the loop of the binding pocket [6]. While IclR members appear to share common architecture, variations in the relative orientation of the DBDs and LBDs are indicative of the flexibility of the linker connecting these domains and may contribute to the variety of functions and mechanisms of the family [7].…”