Crystal structure of a MATα2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions

The MATα2 homeodomain regulates the expression of cell type-specific genes in yeast. We have determined the 2.7 Å resolution crystal structure of the α2 homeodomain bound to a biologically relevant DNA sequence. The DNA in this complex is contracted primarily by the third of three α-helices, with additional contacts coming from an N-terminal arm. Comparison of the yeast α2 and the Drosophila engrailed homeodomain-DNA complexes shows that the protein fold is highly conserved, despite a 3-residue insertion in α2 and only 27% sequence identity between the two homeodomains. Moreover, the orientation of the recognition helix on the DNA is also conserved. This docking arrangement is maintained by side chain contacts with the DNA - primarily the sugar-phosphate backbone - that are identical in α2 and engrailled. Since these residues are conserved among all homeodomains, we propose that the contacts with the DNA are also conserved and suggest a general model for homeodomain-DNA interactions.