A molecular model of the inducer binding domain of the galactose repressor of Escherichia coli.

The C-terminal inducer binding domain of the Escherichia coli galactose repressor (GalR) is homologous to several periplasmic chemoreceptor proteins whose three-dimensional structures have been determined at high resolution (Vyas, N. K., Vyas, M. N., and Quiocho, F. A. (1991) J. Biol. Chem. 266, 5226-5237; Mowbray, S. L. and Cole, L. B. (1992) J. Mol. Biol. 225, 155-175). The protein backbone was constructed from the coordinates of glucose/galactose-binding protein using the Homology program (Biosym Technologies, San Diego). Loops were built by searching for substructures in the structure data base, and the side chains were built using a rotamer-base program. A small amount of energy minimization relieved steric strain within the model. The GalR model that has been constructed is consistent with the principles of protein structure; values obtained for the compactness and buried surface area of the model compare favorably with those determined for the chemoreceptor protein structures. The model is consistent with, and provides structural interpretations for, experimental results obtained from physical and biochemical studies. Predictions are made concerning the residues conferring the specificity of galactose induction of GalR and for self-association to dimers. The model provides a first step toward correlating the structure and regulation of GalR and in determining the chemistry of its homologous and heterologous interactions that are critical to its role as a regulator of transcription initiation.