The helix-turn-helix DNA binding motif

Abstract

One of the most striking findings to emerge from the determinations of the structures of Cro, CAP, and X-repressor (1-3) was that these three sequence-specific DNA-binding proteins had in common a substructure now named the helix-turn-helix motif. The apparent importance of this motif was suggested not only by its striking similarity in the respective structures (4,5) but also from amino acid sequence comparisons (6-11) which indicated that a similar motif might occur in other DNA-biding proteins. It was proposed (1,3, 12-14) that the helix-turn-helix motif interacts with operator DNA in a manner simiiar to that shown in Fig. 1 for Cro. Recognition of a specific sequence on DNA was thought to be achieved by a network of hydrogen bonds and other contacts between the side chains of the protein and the parts of the base pairs exposed within the grooves of the DNA. The second helix of the helix-turn-helix motif, which was thought to bind withii the major groove of the DNA, was presumed to be especially important in recognition. The importance of the helix-turn-helix motif in DNA-protein interaction has been supported by a wealth of biochemical and genetic evidence (e.g. see Refs. 15-18) and has now been shown directly by recent structure determinations of a number of complexes of repressor proteins with synthetic operators. These include the DNA-binding domains of the repressors of phage 434 (19,20) and phage X (21), Cro protein from phage 434 (22), and trp repressor from Escherichia coli (23). In each case the helix-turn-helix motif is an integral part of the protein-DNA interface with the second a-helix (the “recognition helix”) located within the major groove of the DNA (cf. Fig. 1). The purpose of this report is not o review, in detail, the structures of these repressor-operator complexes. Rather, we will first discuss the use of amino acid sequence comparisons to locate putative helixturn-helix motifs. Then we will review the structural correspondence between known helii-turn-helix units. Finally, the role of the heliiturn-helix in recognition of sequence-specific binding sites on DNA will be evaluated in light of the recently defined repressor-operator complexes.