CONSERVATION AND DIVERSIFICATION IN HOMEODOMAIN-DNA INTERACTIONS - A COMPARATIVE GENETIC-ANALYSIS

Nearly all metazoan homeodomains (HDs) possess DNA binding targets tha t are related by the presence of a TAAT sequence. We use an in vitro g enetic DNA binding site selection assay to refine our understanding of the amino acid determinants for the recognition of the TAAT site. Sup erimposed upon the conserved ability of metazoan HDs to recognize a TA AT core is a difference in their preference for the bases that lie imm ediately 3' to it. Amino acid position 50 of the HD has been shown to discriminate among these base pairs, and structural studies have sugge sted that water-mediated hydrogen bonds and van der Waals contacts und erlie for this ability. Here, we show that each of six amino acids tes ted at position 50 can confer a distinct DNA binding specificity.