NMR studies of the human retinoic acid receptor-beta DNA-binding domain. Metal coordination and three-dimensional structure

The DNA binding domain of hepatocyte nuclear factor 4 mediates cooperative, specific binding to DNA and heterodimerization with the retinoid X receptor alpha

We recently showed that hepatocyte nuclear factor 4 (HNF-4) defines a unique subclass of nuclear receptors that exist in solution and bind DNA elements as homodimers (Jiang, G., Nepomuceno, L., Hopkins, K., and Sladek, F. M. (1995) Mol. Cell. Biol. 15, 5131-5143). In this study, we show that the dimerization domains of HNF-4 map to both the DNA binding and the ligand binding domain. Whereas the latter is critical for dimerization in solution, the DNA binding domain mediates cooperative, specific binding to direct repeats of AGGTCA separated by one or two nucleotides. Whereas amino acid residues 117-125 (the T-box/third helix region) are insufficient for cooperative homodimerization and high affinity DNA binding, residues 126-142 (encompassing the A-box region) are required. Finally, in contrast to the full-length receptor, the DNA binding domain of HNF-4 is capable of heterodimerizing with that of the retinoid X receptor alpha but not with that of other receptors. These results indicate that the HNF-4 DNA binding domain is distinct from that of other receptors and that the determinants that prevent HNF-4 from heterodimerizing with RXR lie outside the DNA binding domain, presumably in the ligand binding domain.