High-resolution solution structure of the retinoid X receptor DNA-binding domain

The retinoid X receptor (RXR) is a member of the nuclear hormone receptor superfamily of transcriptional regulators and plays a central role in the retinoid and, through its ability to heterodimerize with other nuclear hormone receptors, non-steroid signaling pathways. The DNA-binding and recognition functions of RXR are located in a conserved 83 amino acid residue domain that recognizes the consensus sequence AGGTCA. In order to provide a detailed picture of its structure, we have calculated a high-resolution solution structure of the C195A RXRalpha DNA-binding domain. Structures were calculated using 1131 distance and dihedral angle constraints derived from 1H, 13C and 15N NMR spectra. The structures reveal a perpendicularly packed, "loop-helix" fold similar to other nuclear hormone receptor DNA-binding domains and confirm the existence of the C-terminal helix, which was first observed in the low-resolution NMR structure. The C-terminal helix is well formed and is stabilized by packing interactions with residues in the hydrophobic core. The solution structure of RXR is very similar to that determined by X-ray crystallographic studies of the RXR-TR heterodimer complex with DNA, except that in the latter case no electron density was observed for residues corresponding to the C-terminal helix. Other differences between the X-ray and NMR structures occur in the second zinc-binding loop, which is disordered in solution. Heteronuclear 15N NOE measurements suggest that this loop has enhanced flexibility in the free protein.