At the Cutting EdgeLooking at nuclear receptors from a new angle
Graphical abstract
Introduction
Nuclear receptors (NRs) play a crucial role in many physiological processes such as reproduction, metabolism, inflammation, immunity and lipid signaling (Hollman et al., 2012, Lamers et al., 2012, Pascual-Garcia and Valledor, 2012, Verhoeven et al., 2010). As much as 48 human NRs have been identified thus far (Xiao et al., 2013). Nuclear receptors are activated by their cognate ligands or other signals and function as transcription factors. Upon activation, the NR will bind to a specific DNA sequence, named the response element, located in the regulatory regions of their target genes.
When binding to the promoter or enhancer regions of the target genes, the receptor will affect transcription by recruiting specific co-regulators and components of the transcription initiation complex or RNA polymerase II (Acevedo and Kraus, 2004).
Detailed insight in the structure–function relationship of NRs originates from crystallographic studies on the two most conserved domains: the DNA binding domain (DBD) and the ligand binding domain (LBD). The aminoterminal domains of NRs are highly variable in length and in sequence. Structural studies indicate they are flexible and most likely intrinsically disordered (Khan et al., 2011, Kumar and Litwack, 2009, Kumar and Thompson, 2012). The hinge regions which connect the DNA- with the ligand-binding domains are the least conserved between the members of the NR family and their structures are poorly understood.
Crystallographic data for receptor dimers binding to DNA as well as coactivator peptides have now been reported for the PPARγ (peroxisome proliferator-activated receptor)–RXRα (retinoid X receptor) heterodimer and for the HNF-4α (hepatocyte nuclear factor 4) homodimer (Chandra et al., 2008, Chandra et al., 2013). Solution structures of several receptor heterodimers were obtained via small-angle X-ray scattering (SAXS), small-angle neutron scattering (SANS) and electron-microscopy (EM) (Rochel et al., 2011). Here, we focus on how these different structures can be reconciled and what novel insights and questions are evoked by them, with regard to steroid receptor action.
Section snippets
DNA binding by nuclear receptors
Extensive study of DNA binding by NRs has shown that the global composition of the DNA response element determines which NR can bind to it. Response elements are typically composed of two hexameric sequence organized as a direct, inverted or everted repeat. Each hexameric sequence or half-site is recognized by a receptor (Roemer et al., 2006). The half-sites are usually separated from each other by a spacer with variable length. Less common are response elements that consist of only 1 hexameric
The ligand-binding domain
The 3-dimensional structure of the LBD consists of 12 α-helices in antiparallel sandwich-like arrangement (Wurtz et al., 1996). A comparison of the structures in absence and in presence of hormone led to the ‘mouse trap’ hypothesis (Parker and White, 1996) which was later confirmed by the structures of many NR-LBDs. When an agonist binds the ligand-binding pocket, helix 12 serves as a lid and covers the ligand-binding pocket. This repositioned helix 12 forms a platform for coactivator binding (
Allosteric communication in nuclear receptors
Nuclear receptors are modular proteins composed of different domains that enable the receptor to fulfill its function as ligand-activated transcription factor (Claessens et al., 2008). Despite the fact that the domains can execute their prime functions of transactivation, DNA and ligand binding in isolation, there is experimental evidence for functional communications between the different domains. For the GR for instance, the lever arm in the DBD is responsible for mediating communication from
Structural data supporting domain communications
The group of Rastinejad reported the first crystal structure of full size nuclear receptors, they observed a closed conformation for the PPARγ–RXRα heterodimer (Fig. 3, Fig. 4) (Chandra et al., 2008). The fold and dimerizations of the DBDs and the LBDs are similar to those of isolated DBDs and LBDs reported earlier, and each of the liganded LBDs was bound by one LXXLL coactivator peptide (Connors et al., 2009, Gampe et al., 2000, Holmbeck et al., 1998). Unfortunately, the structure of the NTDs
The open/extended conformation of DNA-bound receptor dimers
The group of Moras used SAXS, SANS and FRET (Fluorescence resonance energy transfer) to analyze the solution structures of DNA bound full size receptors. They reported an open conformation for several non-steroid receptors (homodimers and heterodimers with RXR; Fig. 3) (Orlov et al., 2012, Osz et al., 2012a, Osz et al., 2012b, Rochel et al., 2011). On the same DNA response element as used for the crystal structure (DR1), the PPAR–RXR heterodimer forms an elongated asymmetric shape with the LBDs
How to reconcile the new data?
Different techniques have led to two apparent contradictory conformations for PPARγ–RXRα. Should we assume that the existence of both an extended and a closed conformation for the PPARγ–RXRα dimer underlines the general flexibility of the multi-domain NRs? (Brelivet et al., 2012, Chandra et al., 2008, Osz et al., 2012b). Both conformations could indeed support different aspects of receptor functioning. While the open conformation allows coregulators and other proteins to interact with the
Structural extrapolation to other nuclear receptors
Hetereodimeric receptor complexes with RXR as binding partner are likely to be similar to each other since both DBD- and LBD-dimerizations are present and these determine the overall structure of the heterodimer. As a promiscuous binding partner, the structure of the RXR hinge region is more variable, while the hinges of other NRs are more structured to specifically select the specific response element for high affinity binding. For instance, because VDR–VDR and VDR–RXR dimers both bind DR3
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