Structure of the yeast a1/α2 homeodomain heterodimer bound to dna

The α2 represser is a homeodomain protein that participates in the determination of yeast mating type. In diploid cells, α2 interacts with the al homeodomain protein to form a heterodimer that binds to DNA sites upstream of haploid-specific genes. We have determined the crystal structure of an a1/α2/DNA ternary complex at a resolution of 2.5 Å. In the a1/α2/DNA complex, the al and α2 homeodomains bind in tandem to one face of the DNA, which contains a 60° bend. Heterodimer contacts are mediated entirely by the C-terminal tail of α2, which is well-ordered only in the presence of the a 1 protein. Part of the α2 tail forms a short amphipathic helix that packs with its hydrophobic face lying in a hydrophobic patch between helices 1 and 2 of al. Despite the interactions with al and the distortion induced in the DNA, α2 in the ternary complex forms essentially the same contacts with the DNA as it does when binding on its own. Based on our study of the a1/α2 heterodimer, we present a model for complex formation between the Oct-1 POU-domain protein, and VP-16, a herpesvirus transcriptional activator.