A molecular code dictates sequence-specific DNA recognition by homeodomains.
Most homeodomains bind to DNA sequences containing the motif 5'-TAAT-3'. The homeodomain of thyroid transcription factor 1 (TTF-1HD) binds to sequences containing a 5'-CAAG-3' core motif, delineating a new mechanism for differential DNA recognition by homeodomains. We investigated the molecular basis of the DNA binding specificity of TTF-1HD by both structural and functional approaches. As already suggested by the three-dimensional structure of TTF-1HD, the DNA binding specificities of the TTF-1, Antennapedia and Engrailed homeodomains, either wild-type or mutants, indicated that the amino acid residue in position 54 is involved in the recognition of the nucleotide at the 3' end of the core motif 5'-NAAN-3'. The nucleotide at the 5' position of this core sequence is recognized by the amino acids located in position 6, 7 and 8 of the TTF-1 and Antennapedia homeodomains. These data, together with previous suggestions on the role of amino acids in position 50, indicate that the DNA binding specificity of homeodomains can be determined by a combinatorial molecular code. We also show that some specific combinations of the key amino acid residues involved in DNA recognition do not follow a simple, additive rule.
Damante
G
G
Dipartimento di Scienze e Tecnologie Biomediche, Università di Udine, Italy.
Pellizzari
L
L
Esposito
G
G
Fogolari
F
F
Viglino
P
P
Fabbro
D
D
Tell
G
G
Formisano
S
S
Di Lauro
R
R
D000818:Animals; D051943:Antennapedia Homeodomain Protein; D004247:DNA / Q000378:metabolism*; D004330:Drosophila; D029721:Drosophila Proteins; D018398:Homeodomain Proteins / Q000378:metabolism*; D007301:Insect Hormones / Q000378:metabolism; D008958:Models, Molecular; D016297:Mutagenesis, Site-Directed; D009687:Nuclear Proteins / Q000378:metabolism; D017434:Protein Structure, Tertiary; D013329:Structure-Activity Relationship; D000074482:Thyroid Nuclear Factor 1; D014157:Transcription Factors / Q000378:metabolism
D051943:Antennapedia Homeodomain Protein; C497974:Antp protein, Drosophila; D029721:Drosophila Proteins; C063459:En protein, Drosophila; D018398:Homeodomain Proteins; D007301:Insect Hormones; D009687:Nuclear Proteins; D000074482:Thyroid Nuclear Factor 1; D014157:Transcription Factors; D004247:DNA