Conservation and diversification in homeodomain-DNA interactions: a comparative genetic analysis.
Nearly all metazoan homeodomains (HDs) possess DNA binding targets that are related by the presence of a TAAT sequence. We use an in vitro genetic DNA binding site selection assay to refine our understanding of the amino acid determinants for the recognition of the TAAT site. Superimposed upon the conserved ability of metazoan HDs to recognize a TAAT core is a difference in their preference for the bases that lie immediately 3' to it. Amino acid position 50 of the HD has been shown to discriminate among these base pairs, and structural studies have suggested that water-mediated hydrogen bonds and van der Waals contacts underlie for this ability. Here, we show that each of six amino acids tested at position 50 can confer a distinct DNA binding specificity.
Wilson
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Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10021, USA.
Sheng
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G
Jun
S
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Desplan
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C
D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D017124:Conserved Sequence; D016054:DNA, Protozoan / Q000737:chemistry* / Q000378:metabolism*; D056890:Eukaryota / Q000378:metabolism*; D014644:Genetic Variation; D005982:Glutathione Transferase / Q000096:biosynthesis; D018398:Homeodomain Proteins / Q000096:biosynthesis / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis; D017433:Protein Structure, Secondary; D011993:Recombinant Fusion Proteins / Q000096:biosynthesis / Q000737:chemistry / Q000378:metabolism; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity
D016054:DNA, Protozoan; D018398:Homeodomain Proteins; D009838:Oligodeoxyribonucleotides; D011993:Recombinant Fusion Proteins; D005982:Glutathione Transferase