Evidence that the DNA binding specificity of winged helix proteins is mediated by a structural change in the amino acid sequence adjacent to the principal DNA binding helix

We present the first structural evidence supporting the hypothesis that the binding specificity of the winged helix DNA binding motif is mediated by residues adjacent to the alpha-helix (H3), the moiety which is primarily involved in the interaction with DNA. Using NMR to determine secondary structural elements of a winged helix family member, Genesis (formerly HFH-2), and comparing these with those found in the X-ray crystal structure of the HNF-3 gamma/DNA complex [Clark, K. L., Halay, E, D., Lai, E,, & Burley, S. K. (1993) Nature 364, 412-420], we show that the major differences observed occur for H3 and the region immediately prior to this. H3 in Genesis is slightly shorter than in HNF-3 gamma and, in addition, we observe an extra small helix (H4) in the region between H2 and H3 which is not found in the HNF-3 gamma/DNA complex. This is significant as it has been shown previously [Overdier, D. G., Porcella, A., & Costa R. H. (1994) Mel. Cell. Biol. 14, 2755-2766] that the DNA-binding specificity is influenced by amino acid residues in this region.