DIFFERENTIAL ORIENTATIONS OF THE DNA-BINDING DOMAIN AND CARBOXY-TERMINAL DIMERIZATION INTERFACE REGULATE BINDING-SITE SELECTION BY NUCLEAR RECEPTOR HETERODIMERS

Retinoic acid, thyroid hormone, and vitamin D receptors preferentially activate target genes through response elements that consist of direc t repeat arrangements of a core recognition motif of consensus sequenc e AGGTCA. We present evidence that the preference for direct repeat el ements arises from two fundamental differences from steroid hormone re ceptors. First, retinoic acid, thyroid hormone, and vitamin D receptor s are demonstrated to preferentially form heterodimers with the retino id X receptors. These interactions are mediated by the carboxy-termina l dimerization interface, with heterodimer preference specified by act ions of the DNA-binding domain. Second, the DNA-binding domains of het erodimeric receptors appear to be rotationally flexible with respect t o the carboxy-terminal dimerization interface. Several independent lin es of evidence suggest that, relative to the retinoid X and steroid ho rmone receptors, the DNA-binding domain of the thyroid hormone recepto r is preferentially rotated by approximately 180-degrees with respect to its carboxy-terminal dimerization interface. As a result, solution interactions between the carboxy-terminal dimerization interfaces of t he retinoid X and thyroid hormone receptors are predicted to lead to t he preferential alignment of their respective DNA-binding domains in a direct repeat configuration. This alignment would position the retino id X receptor over the upstream recognition motif of direct repeat res ponse elements. Differential orientations of the DNA-binding domain, w hich contribute to the polarity of heterodimer binding, are regulated by a short sequence (the A box) that is located between the conserved DNA-binding and carboxy-terminal dimerization domains.