Residues important for the function of a multihelical DNA binding domain in the new transcription factor family of Cam and Tet repressors

We report that some prokaryotic repressors including CamR and TetR belong to the same family. CamR and TetR bind to DNA using a multihelical DNA binding domain (DBD) at the N-termini of the proteins, while the C-termini are important for regulating the DNA binding in a manner dependent on their co-factors (camphor for CamR, tetracycline for TetR). In all, 11 important amino acid positions have been identified in the CamR DBD by the systematic substitution of residues by Ala. Of the 11 positions, 10 are either buried in the core, and thus important for creating the hydrophobic environment, or exposed on the surface, and thus important for binding to DNA. The eleventh residue, Gly, seems to be important for a loop structure. The DNA binding mode of this type of DBD and a general mechanism of regulating their DNA binding are discussed in reference to the crystal structure of TetR [Hinrichs et al., (1994) Science, 264, 418-420].