title: 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.
abstract: 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-3gamma/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-3gamma and, in addition, we observe an extra small helix (H4) in the region between H2 and H3 which is not found in the HNF-3gamma/DNA complex. This is significant as it has been shown previously [Overdier, D. G., Porcella, A., & Costa R. H. (1994) Mol. Cell. Biol. 14, 2755-2766] that the DNA-binding specificity is influenced by amino acid residues in this region.
authors.affiliation: Department of Biochemistry, University of Illinois at Chicago, 1819 W. Polk Street, Chicago, Illinois 60612, USA.
authors.forename: I
authors.initials: I
authors.lastname: Marsden
authors.forename: Y
authors.initials: Y
authors.lastname: Chen
authors.forename: C
authors.initials: C
authors.lastname: Jin
authors.forename: X
authors.initials: X
authors.lastname: Liao
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D000818:Animals; D017124:Conserved Sequence; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics*; D051858:Forkhead Transcription Factors; D019077:Helix-Turn-Helix Motifs / Q000235:genetics*; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D011485:Protein Binding / Q000235:genetics; D017433:Protein Structure, Secondary; D051381:Rats; D012097:Repressor Proteins / Q000737:chemistry* / Q000235:genetics*
chemical_list: D004268:DNA-Binding Proteins; D051858:Forkhead Transcription Factors; C491100:Foxd3 protein, rat; D012097:Repressor Proteins; D004247:DNA