IN THE TTF-1 HOMEODOMAIN THE CONTRIBUTION OF SEVERAL AMINO-ACIDS TO DNA RECOGNITION DEPENDS ON THE BOUND SEQUENCE

The thyroid transcription factor-1 homeodomain (TTF-1HD) shows a pecul iar DNA binding specificity, preferentially recognizing sequences cont aining the 5'-CAAG-3' core motif, Most other homeodomains instead reco gnize sites containing the 5'-TAAT-3' core motif, Here, we show that T TF-1HD efficiently recognizes another sequence, called D1, devoid of t he 5'-CAAG-3' core motif, Different experimental approaches indicate t hat TTF-1HD contacts the D1 sequence in a manner which is different to that used to interact with sequences containing the 5'-CAAG-3' core m otif, The binding activities that mutants of TTF-1HD display with the D1 sequence or with the sequence containing the 5'-CAAG-3' core motif indicate that the role of several DMA-contacting amino acids is differ ent, In particular,during recognition of the D1 sequence, backbone-int eracting amino acids not relevant in binding to sequences containing t he 5'-CAAG-3' core motif play an important role, In the TTF-1HD, there fore, the contribution of several amino acids to DNA recognition depen ds on the bound sequence, These data indicate that although a common b onding network exists in all of the HD/DNA complexes, peculiarities im portant for DNA recognition may occur in single cases.