Altered DNA Recognition and Bending by Insertions in the α2 Tail of the Yeast a1/α2 Homeodomain Heterodimer

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Abstract
The yeast MATα2 and MATa1 homeodomain proteins bind cooperatively as a heterodimer to sites upstream of haploid-specific genes, repressing their transcription. In the crystal structure of α2 and a1 bound to DNA, each homeodomain makes independent base-specific contacts with the DNA and the two proteins contact each other through an extended tail region of α2 that tethers the two homeodomains to one another. Because this extended region may be flexible, the ability of the heterodimer to discriminate among DNA sites with altered spacing between α2 and a1 binding sites was examined. Spacing between the half sites was critical for specific DNA binding and transcriptional repression by the complex. However, amino acid insertions in the tail region of α2 suppressed the effect of altering an a1/α2 site by increasing the spacing between the half sites. Insertions in the tail also decreased DNA bending by a1/α2. Thus tethering the two homeodomains contributes to DNA bending by a1/α2, but the precise nature of the resulting bend is not essential for repression.