Thyroid hormone receptors (TRs) bind as homodimers or heterodimers with retinoid X receptors (RXRs) to DNA elements with diverse orientations of AGGTCA half-sites. We performed a comprehensive x-ray crystal structure-guided mutation analysis of the TR ligand binding domain (TR LBD) surface to map the functional interface for TR homodimers and heterodimers with RXR in the absence and/or in the presence of DNA. We also identified the molecular contacts in TR LBDs crystallized as dimers. The results show that crystal dimer contacts differ from those found in the functional studies. We found that identical TR LBD residues found in helices 10 and 11 are involved in TR homodimerization and heterodimerization with RXR. Moreover, the same TR LBD surface is operative for dimerization with direct repeats spaced by 4 base pairs (DR-4) and with the inverted palindrome spaced by 6 base pairs (F2), but not with TREpal (unspaced palindrome), where homodimers appear to be simply two monomers binding independently to DNA. We also demonstrate that interactions between the TR and RXR DNA binding domains stabilize TR-RXR heterodimers on DR-4. The dimer interface can be functional in the cell, because disruption of key residues impairs transcriptional activity of TRs mediated through association with RXR LBD linked to GAL4 DNA-binding domain.Thyroid hormone receptors (TRs) 1 are members of the nuclear receptor superfamily, which includes receptors for steroid hormones, vitamins, retinoids, prostaglandins, fatty acids, and orphan receptors for which no ligands are known (1-4). These receptors are modular transcription factors that bind to specific sequences in promoters of target genes. They bind DNA as monomers, homodimers, or heterodimers through the DNA binding domain (DBD) (1, 5). Steroid receptors bind as homodimers to two half-sites of a DNA palindrome. In contrast, TRs, retinoic acid receptors (RARs), vitamin D receptors (VDRs), peroxisome proliferator-activated receptors (PPARs), and several orphan receptors bind as heterodimers with retinoid X receptors (RXRs) to direct repeats (DRs) of the AGGTCA half-site (1) but also bind to elements oriented as palindromes or inverted palindromes (1). Binding specificity of these receptors is determined by spacing between the half-sites, because PPARs, VDRs, TRs, and RARs bind preferentially to DRs spaced by 1, 3, 4, or 5 nucleotides, respectively (1). Unlike PPARs, VDRs, and RARs, TRs also bind DNA as monomers and as homodimers to DRs and to inverted palindromes spaced by 4 -6 nucleotides (F2) (1, 6, 7). Current concepts of the dimerization and heterodimerization interfaces for nuclear receptors are based on mutational and x-ray crystal structural data. The mutation data for LBDs are mostly limited to TR, RAR, VDR, and RXR. Little is known from mutation studies with the steroid receptors, because only few studies report single mutations in the LBDs that disrupt dimerization (8). This is due in part to the fact that the DBDs and amino-terminal fragments of these receptors contribute su...