At the Cutting Edge
Looking at nuclear receptors from a new angle

https://doi.org/10.1016/j.mce.2013.09.009Get rights and content

Highlights

  • Nuclear receptor–DNA complexes are highly dynamic: open or closed conformation.

  • Both heterodimeric and homodimeric receptors form asymmetric DNA binding complexes.

  • An intimate contact between different domains determines receptor activity on DNA.

Abstract

While the structures of the DNA- and ligand-binding domains of many nuclear receptors have been determined in great detail; the mechanisms by which these domains interact and possibly ‘communicate’ is still under debate. The first crystal structures of receptor dimers bound to ligand, DNA and coactivator peptides provided new insights in this matter. The observed binding modes revealed exciting new interaction surfaces between the different nuclear receptor domains. Such interfaces are proposed to be the route through which allosteric signals from the DNA are passed on to the ligand-binding domain and the activating functions of the receptor. The structural determinations of DNA-bound receptor dimers in solution, however, revealed an extended structure of the receptors. Here, we discuss these apparent contradictory structural data and their possible implications for the functioning of nuclear receptors.

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

References (102)

  • R.T. Gampe et al.

    Asymmetry in the PPARgamma/RXRalpha crystal structure reveals the molecular basis of heterodimerization among nuclear receptors

    Mol. Cell

    (2000)
  • M.D. Gearhart et al.

    Monomeric complex of human orphan estrogen related receptor-2 with DNA: a pseudo-dimer interface mediates extended half-site recognition

    J. Mol. Biol.

    (2003)
  • H. Greschik et al.

    Structural basis for the deactivation of the estrogen-related receptor gamma by diethylstilbestrol or 4-hydroxytamoxifen and determinants of selectivity

    J. Biol. Chem.

    (2004)
  • N. Heldring et al.

    Structural insights into corepressor recognition by antagonist-bound estrogen receptors

    J. Biol. Chem.

    (2007)
  • C. Helsen et al.

    Structural basis for nuclear hormone receptor DNA binding

    Mol. Cell. Endocrinol.

    (2012)
  • D.A. Hollman et al.

    Anti-inflammatory and metabolic actions of FXR: insights into molecular mechanisms

    Biochim. Biophys. Acta

    (2012)
  • S.M. Holmbeck et al.

    High-resolution solution structure of the retinoid X receptor DNA-binding domain

    J. Mol. Biol.

    (1998)
  • M.H. Hsu et al.

    A carboxyl-terminal extension of the zinc finger domain contributes to the specificity and polarity of peroxisome proliferator-activated receptor DNA binding

    J. Biol. Chem.

    (1998)
  • R. Kumar et al.

    Structural and functional relationships of the steroid hormone receptors’ N-terminal transactivation domain

    Steroids

    (2009)
  • R. Kumar et al.

    Folding of the glucocorticoid receptor N-terminal transactivation function: dynamics and regulation

    Mol. Cell Endocrinol.

    (2012)
  • E. Margeat et al.

    Ligands differentially modulate the protein interactions of the human estrogen receptors alpha and beta

    J. Mol. Biol.

    (2003)
  • G.A. Schoch et al.

    Molecular switch in the glucocorticoid receptor: active and passive antagonist conformations

    J. Mol. Biol.

    (2010)
  • T. Sone et al.

    Vitamin D receptor interaction with specific DNA. Association as a 1,25-dihydroxyvitamin D3-modulated heterodimer

    J. Biol. Chem.

    (1991)
  • G.S. Takimoto et al.

    Functional properties of the N-terminal region of progesterone receptors and their mechanistic relationship to structure

    J. Steroid Biochem. Mol. Biol.

    (2003)
  • D.J. van de Wijngaart et al.

    Androgen receptor coregulators: recruitment via the coactivator binding groove

    Mol. Cell Endocrinol.

    (2012)
  • M.A. van Tilborg et al.

    Mutations in the glucocorticoid receptor DNA-binding domain mimic an allosteric effect of DNA

    J. Mol. Biol.

    (2000)
  • A. Warnmark et al.

    The N-terminal regions of estrogen receptor alpha and beta are unstructured in vitro and show different TBP binding properties

    J. Biol. Chem.

    (2001)
  • J. Yang et al.

    Interactions of the mineralocorticoid receptor – within and without

    Mol. Cell Endocrinol.

    (2012)
  • M.L. Acevedo et al.

    Transcriptional activation by nuclear receptors

    Essays Biochem.

    (2004)
  • F. Alimirah et al.

    Functionality of unliganded VDR in breast cancer cells: repressive action on CYP24 basal transcription

    Mol. Cell Biochem.

    (2010)
  • T. Almlof et al.

    Role of important hydrophobic amino acids in the interaction between the glucocorticoid receptor tau 1-core activation domain and target factors

    Biochemistry

    (1998)
  • M. Anbalagan et al.

    Post-translational modifications of nuclear receptors and human disease

    Nucl. Recept. Signal.

    (2012)
  • W. Bourguet et al.

    Crystal structure of the ligand-binding domain of the human nuclear receptor RXR-alpha

    Nature

    (1995)
  • J. Brodie et al.

    Intra-domain communication between the N-terminal and DNA-binding domains of the androgen receptor: modulation of androgen response element DNA binding

    J. Mol. Endocrinol.

    (2005)
  • J.B. Bruning et al.

    Coupling of receptor conformation and ligand orientation determine graded activity

    Nat. Chem. Biol.

    (2010)
  • A.M. Brzozowski et al.

    Molecular basis of agonism and antagonism in the oestrogen receptor

    Nature

    (1997)
  • L. Callewaert et al.

    Interplay between two hormone-independent activation domains in the androgen receptor

    Cancer Res.

    (2006)
  • C. Carlberg et al.

    Two nuclear signalling pathways for vitamin D

    Nature

    (1993)
  • V. Cavailles et al.

    Interaction of proteins with transcriptionally active estrogen receptors

    Proc. Natl. Acad. Sci. USA

    (1994)
  • V. Chandra et al.

    Structure of the intact PPAR-gamma-RXR-nuclear receptor complex on DNA

    Nature

    (2008)
  • V. Chandra et al.

    Multidomain integration in the structure of the HNF-4alpha nuclear receptor complex

    Nature

    (2013)
  • J.H. Choi et al.

    Anti-diabetic drugs inhibit obesity-linked phosphorylation of PPARgamma by Cdk5

    Nature

    (2010)
  • F. Claessens et al.

    Diverse roles of androgen receptor (AR) domains in AR-mediated signaling

    Nucl. Recept. Signal.

    (2008)
  • A.R. Daniel et al.

    The progesterone receptor hinge region regulates the kinetics of transcriptional responses through acetylation, phosphorylation, and nuclear retention

    Mol. Endocrinol.

    (2012)
  • S. Denayer et al.

    The rules of DNA recognition by the androgen receptor

    Mol. Endocrinol.

    (2010)
  • P. Doesburg et al.

    Functional in vivo interaction between the amino-terminal, transactivation domain and the ligand binding domain of the androgen receptor

    Biochemistry

    (1997)
  • H. Dotzlaw et al.

    The amino terminus of the human AR is target for corepressor action and antihormone agonism

    Mol. Endocrinol.

    (2002)
  • S. Garcia-Vallve et al.

    Nuclear receptors, nuclear-receptor factors, and nuclear-receptor-like orphans form a large paralog cluster in Homo sapiens

    Mol. Biol. Evol.

    (1998)
  • A.S. Garza et al.

    Binding-folding induced regulation of AF1 transactivation domain of the glucocorticoid receptor by a cofactor that binds to its DNA binding domain

    PLoS One

    (2011)
  • S. Grosdidier et al.

    Allosteric conversation in the androgen receptor ligand-binding domain surfaces

    Mol. Endocrinol.

    (2012)
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