Differential role of homologous positively charged amino acid residues for ligand binding in retinoic acid receptor alpha compared with retinoic acid receptor beta

The diverse biological actions of retinoic acid (RA) are mediated by retinoic acid receptors (RARs) and retinoid X receptors, Although it has been suggested that the ligand binding domains (LBDs) of RARs share the same novel folding pattern, many RAR subtype-specific agonists and antagonists have been synthesized demonstrating that the LED of each RAR subtype has unique features. We have examined the role of several positively charged amino acid residues located in the LBD of RAR alpha in RA binding. These results are compared with previously published data for the homologous mutations in RAR beta, Lys(227) of RAR alpha does not appear to be important for RA binding or RA-dependent transactivation, whereas the homologous residue in RAR beta, Lys(220), plays an important synergistic role with Arg(269) in these two activities. In addition, Arg(276) of RAR alpha, like its homologous residue Arg(269) of RAR beta, was found to play an important role in the binding of RA most likely by interacting with the carboxylate group of RA, However, the orientation of and electronic environment associated with Arg(276) in RAR alpha appears to be different from that of Arg(269) in RAR beta, thus contributing to the uniqueness of the ligand binding pocket of each receptor.