A classic example of bifunctional transcription factors is the family of Nuclear Receptor (NR) proteins. These are DNA-binding transcription factors that bind certain hormones, vitamins, and other small, diffusible signaling molecules. The non-liganded NRs recruit specific corepressor complexes of the NCOR/SMRT type, to mediate transcriptional repression of the target genes to which they are bound. During signaling, ligand binding to a specific domain the NR proteins induces a conformational change that results in the exchange of the associated CoR complex, and its replacement by a specific coactivator complex of the TRAP / DRIP / Mediator type. These coactivator complexes typically nucleate around a MED1 coactivator protein that is directly bound to the NR transcription factor.
A general feature of the 49 human NR proteins is that in the unliganded state, they each bind directly to an NCOR corepressor protein, either NCOR1 or NCOR2 (NCOR2 was previously named "SMRT"). This NCOR protein nucleates the assembly of additional, specific corepressor proteins, depending on the cell and DNA context. The NR-NCOR interaction is mediated by a specific protein interaction domain (PID) present in the NRs that binds to specific cognate PID(s) present in the NCOR proteins. Thus, the human NRs each take part in an NR-NCOR binding reaction in the absence of binding by their ligand.
A second general feature of the NR proteins is that they each contain an additional, but different PID that mediates specific binding interactions with MED1 proteins. In the ligand-bound state, NRs each take part in an NR-MED1 binding reaction to form an NR-MED1 complex. The bound MED1 then functions to nucleate the assembly of additional specific coactivator proteins, depending on the cell and DNA context, such as what specific target gene promoter they are bound to, and in what cell type.
The formation of specific MED1-containing coactivator complexes on specific NR proteins has been well-characterized for a number of the human NR proteins (see Table 1 in (Bourbon, 2004)). For example, binding of thyroid hormone (TH) to the human TH Receptor (THRA or THRB) was found to result in the recruitment of a specific complex of Thyroid Receptor Associated Proteins - the TRAP coactivator complex - of which the TRAP220 subunit was later identified to be the Mediator 1 (MED1) homologue.
Similarly, binding of Vitamin D to the human Vitamin D3 Receptor was found to result in the recruitment of a specific complex of D Receptor Interacting Proteins - the DRIP coactivator complex, of which the DRIP205 subunit was later identified to be human MED1.