Other DNA-Binding Motifs

Describe the helix-tum-helix motif and relate it to DNA binding. Note the existence of other DNA-binding motife. 

The DNA-binding motifs discussed in this and the preceding two chapters are those most frequently found in procaryotes and eucaryotes. However, other motifs are known, for example the p sheet motif of the met repressor in Escherichia coli which binds to the major groove of DNA. No doubt others remain to be discovered. 

Dimerization of the Ce-zinc cluster transcription factors involves an a-helical coiled coil in the dimerization region. Coiled coils, often called leucine zippers, are also found in a large group of transcription factors that do not contain zinc. The leucine zipper is made up of two a helices in a coiled coil with every seventh residue leucine or some other large hydrophobic residue, such as isoleucine or valine. Leucine zipper transcription factors (b/zip) include factors characterized by heterodimerization, for example Fos and Jun. The a-helical DNA-binding motifs of the heterodimers recognize quite different base sequences and are continous with the a helices of the zipper. 

A helix-loop-helix motif is a DNA-binding motif, related to the leucine-zipper. A helix-loop-helix motif consists of a short a helix, connected by a loop to a second, longer a helix. The loop is flexible and allows one helix to fold back and pack against the other. The helix-loop-helix structure binds not only DNA but also the helix-loop-helix motif of a second helix-loop-helix protein forming either a homodimer or a heterodimer. 

Aaron Klug discovered the first of the eukaryotic DNA-binding motifs in Xenopus transcription factor IIIA (TFlllA), a protein which binds to the 5S rRNA gene. The resulting complex subsequently binds two other transcription factors and RNA polymerase III, which leads to the initiation of transcription of the 5S rRNA gene. The TFIIIA molecule contains 9 similar 30-residue-long, tandemly repeated modules. Each of these modules contains two invariant Cys residues, two invariant His residues, and several conserved hydrophobic residues (Figure 12.19), and a Zn + ion, which is tetrahedrally coordinated by the invariant Cys and His... 

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