Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex.
Homeodomains are one of the key families of eukaryotic DNA-binding motifs and provide an important model system for studying protein-DNA interactions. We have crystallized the Antennapedia homeodomain-DNA complex and solved this structure at 2.4 A resolution. NMR and molecular dynamics studies had implied that this homeodomain achieves specificity through an ensemble of rapidly fluctuating DNA contacts. The crystal structure is in agreement with the underlying NMR data, but our structure reveals a well-defined set of contacts and also reveals the locations and roles of water molecules at the protein-DNA interface. The synthesis of X-ray and NMR studies provides a unified, general model for homeodomain-DNA interactions.
Fraenkel
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Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA.
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D000595:Amino Acid Sequence; D051943:Antennapedia Homeodomain Protein; D001216:Asparagine / Q000737:chemistry; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D018398:Homeodomain Proteins / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D009687:Nuclear Proteins; D009711:Nucleotides / Q000737:chemistry; D013403:Sugar Phosphates / Q000737:chemistry; D014157:Transcription Factors
D051943:Antennapedia Homeodomain Protein; D004268:DNA-Binding Proteins; D018398:Homeodomain Proteins; D009687:Nuclear Proteins; D009711:Nucleotides; D013403:Sugar Phosphates; D014157:Transcription Factors; D001216:Asparagine; D004247:DNA