Figure 7–8 The binding of a transcription regulator to a specific DNA sequence. On the left, a single contact is shown between a transcription regulator and DnA; such contacts allow the protein to “read” the DnA sequence. On the right, the complete set of contacts between a transcription regulator (a member of the homeodomain family—see panel 7–1) and its cis-regulatory sequence is shown. the DnA-binding portion of the protein is 60 amino acids long. Although the interactions in the major groove are the most important, the protein is also seen to contact both the minor groove and phosphates in the sugar–phosphate DnA backbone. (See C. wolberger et al., Cell 67:517–528, 1991.) tryptophan repressor lambda Cro lambda repressor fragment CAP fragment DNA DNA 3.4 nm (A) Arg C 3 1 2 N 2 Ser Arg Asn 3 1 (B) Originally identifed in bacterial transcription regulators, this motif has since been found in many hundreds of DNA-binding proteins from both eukaryotes and prokaryotes. It is constructed from two ˜ helices (blue and red) connected by a short extended chain of amino acids, which constitutes the “turn.” The two helices are held at a fxed angle, primarily through interactions between the two helices. The more C-terminal helix (in red) is called the recognition helix because it fts into the major groove of DNA; its amino acid side chains, which differ from protein to protein, play an important part in recognizing the specifc DNA sequence to which the protein binds. All of the proteins shown here bind DNA as dimers in which the two copies of the recognition helix (in red) are separated by exactly one turn of the DNA helix (3.4 nm); thus both recognition helices of the dimer can ft into the major groove of DNA. Not long after the frst transcription regulators were discovered in bacteria, genetic analyses of the fruit fy Drosophila led to the characterization of an important class of genes, the homeotic selector genes, that play a critical part in orchestrating fy development (discussed in Chapter 21). It was later shown that these genes coded for transcription regulators that bound DNA through a structural motif named the homeodomain. Two different views of the same structure are shown. (A) The homeodomain is folded into three ˜ helices, which are packed tightly together by hydrophobic interactions. The part containing helices 2 and 3 closely resembles the helix–turn–helix motif. (B) The recognition helix (helix 3, red) forms important contacts with the major groove of DNA. The asparagine (Asn) of helix 3, for example, contacts an adenine, as shown in Figure 7–8. A fexible arm attached to helix 1 forms contacts with nucleotide pairs in the minor groove. The leucine zipper motif is named because of the way the two ˜helices, one from each monomer, are joined together to form a short coiled-coil. These proteins bind DNA as dimers where the two long ˜helices are held together by interactions between hydrophobic amino acid side chains (often on leucines) that extend from one side of each helix. Just beyond the dimerization interface, the two ˜helices separate from each other to form a Y-shaped structure, which allows their side chains to contact the major groove of DNA. The dimer thus grips the double helix like a clothespin on a clothesline. recognition helix recognition helix DNA dimerization interface HELIX–TURN–HELIX PROTEINS HOMEODOMAIN PROTEINS LEUCINE ZIPPER PROTEINS 376 PANEL 7–1: Common Structural Motifs in Transcription Regulators