Repeat of a helix–turn–helix module in DNA-binding proteins

Helix–turn–helix motif is one of the common motifs observed in DNA-binding proteins. The motif interacts with DNA double helix and recognizes specific base sequences. It is assumed that the helix–turn–helix motif appears only once in seven prokaryotic transcriptional repressors of which 3-D structures have been determined by X-ray crystallographk studies. These prokaryotic repressors consist of several a-helices connected with turns. We report here that these repressors are decomposable into helix–turn–helix modules and their connectors. A module is defined as a compact structural unit with consecutive amino acid residues in a globular protein. Each of the helix- turn -helix motifs in the seven proteins corresponds approximately to a single helix-turn—helix module consisting of approximately 13 amino acids. Identification of modules of seven prokaryotic repressors and comparisons of then tertiary structures led to the conclusion that three of these DNA-binding proteins contain more than one helix–turn–helix module with a structure similar to the helix-turn-heUx motif. The difference in module organization of these DNA-binding proteins paves the way for further classification of the DNA-binding proteins with the helix- turn -helix motif. The structural repertoire of these transcriptional regulators was increased through different utilizations in the number of helix–turn–helix and other modules. The difference in DNA base recognition ability in these helix–turn–helix modules is ascribed to a difference in size of a side chain at the fifth residue from Gly, on the turn.