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 t o sequences containing a 5'-CAAG-3' core motif, delineating a new mech anism for differential DNA recognition by homeodomains, We investigate d the molecular basis of the DNA binding specificity of TTF-1HD by bot h structural and functional approaches. As already suggested by the th ree-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 in volved 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 seque nce is recognized by the amino acids located in position 6, 7 and 8 of the TTF-1 and Antennapedia homeodomains, These data, together with pr evious 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 combi nations of the key amino acid residues involved in DNA recognition do not follow a simple, additive rule.