The leucine zipper symmetrically positions the adjacent basic regions for specific DNA binding.

The bZIP structural motif present in several eukaryotic transcription factors is defined by the leucine zipper, a coiled-coil dimerization interface, and an adjacent basic region that directly interacts with DNA. To examine the functional importance of the highly conserved spacing between the leucine zipper and the basic region, we have analyzed the DNA-binding ability of yeast GCN4 proteins containing amino acid insertions between these two subdomains. Proteins containing a surprisingly wide variety of seven-amino acid insertions, but none containing two-, four-, or six-amino acid insertions, are functional. However, heterodimers between wild-type GCN4 and functional derivatives containing seven amino acid insertions are unable to bind DNA. These observations provide strong experimental support for several aspects of the scissors grip and induced fork models for DNA-binding by bZIP proteins. Specifically, they demonstrate that continuous alpha-helices symmetrically diverging from the leucine zipper correctly position the two basic regions for specific binding to abutting DNA half-sites. In addition, the results indicate that GCN4 homodimers are primarily responsible for transcriptional activation in yeast cells.