Three-Dimensional Structure of the Human Retinoic Acid Receptor-β DNA Binding Domain: Implications for DNA-Binding

All-trans-retinoic acid (RA), a vitamin A derivative, plays a crucial role in vertebrate development and differentiation (Thaller & Eichele, 1987). Retinoic acid acts through binding to nuclear retinoic acid receptors (RARs). RARs are members of a superfamily of ligand-inducible nuclear transcription factors which comprises receptors for steroid and thyroid hormones and vitamin D3 (Evans, 1988). Until now three different RAR genes have been identified, RARa, s, and y (Petkovich et al, 1987, Giguere et al., 1987, de The et al., 1987, Brand et al., 1988, Krust et al.. 1989). These proteins are structurally organized in separate domains, labelled A through F (cf. Figure 1). The C domain is the highly conserved DNA-binding domain (DBD) of about 70 amino acid residues and the E domain of about 230 amino acid residues is responsible for ligand binding (Beato, 1989). The C domain recognizes response elements, upstream of receptor target genes. It contains nine conserved cysteine residues, eight of which coordinate two zinc atoms (Beato, 1989). The presence of a zinc binding domain is reminiscent of the “zinc finger” motif found in Xenopus Transcription Factor IIIA (TFIIIA) (Miller et al., 1985) as well as similar domains found in retroviral DNA binding proteins (Green & Berg, 1989) but the DBD of these proteins is structurally different from that of the nuclear hormone receptors (Berg, 1989, Hard et al., 1990, Luisi et al, 1991). The high degree of amino acid sequence homology observed between the RAR DBD and that of other superfamily members (Benbrook et al., 1988) suggests a tertiary fold similar to that found in both the glucocorticoid (Hard et al, 1990) and the estrogen receptors (Schwabe et al., 1990) for which the solution structures have been determined by NMR. Recently, the structure of the GR DBD bound to its response element (RE) as a dimer has been elucidated by X-ray crystallography (Luisi et al., 1991). The mode of binding of the GR DBDs, as seen in the crystal structure of the complex, confirmed models that were proposed for the GR and ER on the basis of their solution structures and biochemical data (Hard et al., 1990, Schwabe et al, 1990). The only difference was an additional short stretch of distorted α-helix observed in the second finger, which appears to be rather flexible in the protein free in solution.