Retinoids exert their physiological action by interacting with two families of nuclear receptors, the retinoic acid receptors (RARs) and the retinoid X receptors (RXRs), which regulate gene expression by forming transcriptionally active heterodimeric RAR/RXR or homodimeric RXR/RXR complexes on DNA. Retinoid receptor activity resides in several regions, including the DNA and ligand binding domains, a dimerization interface, and both a ligand-independent (AF-1) and a ligand-dependent (AF-2) transactivation function. While 9-cis retinoic acid (RA) alone is the cognate ligand for the RXRs, both 9-cis RA and all-trans RA (t-RA) compete for binding with high affinity to the RARs. This latter observation suggested to us that the two isomers may interact with a common binding site. Here we report that RARa has two distinct but overlapping binding sites for 9-cis RA and t-RA. Truncation of a human RARa to 419 amino acids yields a receptor that binds both t-RA and 9-cis RA with high affinity, but truncation to amino acid 404 yields a mutant receptor that binds only t-RA with high affinity. Remarkably, this region also defines a C-terminal boundary for AF-2, as addition of amino acids 405 to 419 restores receptor-mediated gene activity to a truncated human RARRa lacking this region. It is interesting to speculate that binding of retinoid stereoisomers to unique sites within an RAR may function with AF-2 to cause differential activation of retinoid-responsive gene pathways.Retinoic acids (RAs) are derivatives of vitamin A (retinol) which affect a wide spectrum of biological activities, including cellular differentiation and vertebrate development (for a review, see reference 48). These compounds exert their biological action by interacting with two families of nuclear receptors, the RA receptors (RARs) (8,18,27,42) (10,34,53), and the peroxisome proliferator-activated receptor (24,26).On the basis of the amino acid homologies, six regions of functional identity have been described for the members of this superfamily of nuclear receptors (16,19). Regions A and B contain a ligand-independent transactivation function, AF-1, that may play a role in specifying activity on particular target genes (38,39 (3,23,32), while the RARs bind both 9-cis RA and all-trans-RA (t-RA) with high affinity (3). We have shown that 9-cis RA and t-RA compete with each other for binding to the RARs (4), indicating that they share a common binding site. Considering the differences in configuration between 9-cis RA and t-RA, we reasoned that there may be subtle differences in the RAR binding pocket to accommodate both of these ligands. Here we report that in fact, 9-cis RA and t-RA interact with distinct binding determinants on RARc. Using C-terminal truncation mutants of human RARo, we defined a 15-amino-acid region that is absolutely required for 9-cis RA binding but not for high-affinity t-RA binding. Furthermore, we show that these same amino acids are required for the ligand-inducible, receptor-mediated transactivation of 3RARE and identify the AF...