Sub-classification of response regulators using the surface characteristics of their receiver domains.

The omnipresent bacterial switch known as a two-component system is comprised of a response regulator and a sensor kinase with which it interacts. Sensor kinases have been classified and further sub-classified into groups based on their sequence similarity, loop lengths and domain organization. Response regulators have been classified predominantly by the identity and function of their output domains. Here, comparative based homology modeling of the receiver domains of the OmpR sub-family of response regulators in Bacillus subtilis and Escherichia coli suggests further sub-classification is possible. A color-coded scale is used to show trends in surface hydrophobicity. For the OmpR receiver domains modeled these trends allow further sub-classification. The specific surface regions used for this sub-classification procedure correlate with clusters of residues that are important for interaction with cognate four helix bundle HisKA/Hpt domains.