REPEAT OF A HELIX-TURN-HELIX MODULE IN DNA-BINDING PROTEINS

Helix-turn-helix motif is one of the common motifs observed in DNA-bin ding proteins. The motif interacts with DNA double helix and recognize s specific base sequences. It is assumed that the helix - turn - helix motif appears only once in seven prokaryotic transcriptional represso rs of which 3-D structures have been determined by X-ray crystallograp hic studies. These prokaryotic repressors consist of several alpha-hel ices connected with turns. We report here that these repressors are de composable into helix - turn - helix modules and their connectors. A m odule is defined as a compact structural unit with consecutive amino a cid residues in a globular protein. Each of the helix - turn - helix m otifs in the seven proteins corresponds approximately to a single heli x-turn-helix module consisting of approximately 13 amino acids. Identi fication of modules of seven prokaryotic repressors and comparisons of their tertiary structures led to the conclusion that three of these D NA-binding proteins contain more than one helix - turn - helix module with a structure similar to the helix-turn-helix motif. The difference in module organization of these DNA-binding proteins paves the way fo r further classification of the DNA-binding proteins with the helix-tu rn-helix motif. The structural repertoire of these transcriptional reg ulators was increased through different utilizations in the number of helix - turn - helix and other modules. The difference in DNA base rec ognition 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.