The three-dimensional NMR-solution structure of the polypeptide fragment 195-286 of the LFB1/HNF1 transcription factor from rat liver comprises a nonclassical homeodomain.

The three-dimensional backbone fold of a polypeptide fragment from the rat LFB1/HNF1 transcription factor was determined by nuclear magnetic resonance (NMR) spectroscopy in solution. This fragment contains an amino acid sequence that is approximately 22% homologous to the well known homeodomains, but which contains 81 amino acid residues as compared with 60 residues in 'typical' homeodomains. For the present studies we used a recombinant 99 amino acid polypeptide containing this sequence in positions 10-90, which was uniformly labelled with 15N and also doubly labelled with 15N and 13C. The NMR structure of this polypeptide contains three alpha-helices comprising the residues 18-29, 36-50 and 71-84, a loop formed by residues 30-35, and a long stretch of non-regular secondary structure linking the second and third helices. The relative location and orientation of the helices is very similar to that in the Antennapedia (Antp) homeodomain structure, despite the fact that helix II is elongated by about one turn. This confirms a recently advanced hypothesis based on sequence comparisons that this polypeptide segment of LFB1/HNF1 might represent a homeodomain-like structural element. The helix-turn-helix motif, which has been shown to comprise the DNA recognition helix in the Antp homeodomain, can readily be recognized in the LFB1/HNF1 homeodomain, in spite of an extensive modification of the primary structure. The two residues of the tight turn in the Antp homeodomain are replaced by a 23 residue linker region between the two helices in LFB1/HNF1, which bulges out from the rest of the molecule and thus enables the formation of a non-classical helix--turn--helix motif.