Structural basis of RXR-DNA interactions 1 1Edited by P. E. Wright

Zhao, Qiang; Chasse, Scott A.; Devarakonda, Srikripa; Sierk, Michael; Ahvazi, Bijan; Rastinejad, Fraydoon

doi:10.1006/jmbi.1999.3457

Cited by 126 publications

(108 citation statements)

References 51 publications

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“…As importin binding takes place in solution, the findings that the accessibility of the NLS of RXR is regulated by heterodimerization thus further indicate that the LBD exerts a control over the conformation of the DBD. The three-dimensional structures of DNA-bound DBDs and of LBDs of various receptors, including RXR and VDR, have been solved (37)(38)(39)(40). However, insights into the basis of functional communication between the domains has long been hampered by the inability to obtain precise structural information on full-length receptors.…”

Section: Discussionmentioning

confidence: 99%

Nuclear Import of the Retinoid X Receptor, the Vitamin D Receptor, and Their Mutual Heterodimer

Yasmin

Williams

et al. 2005

Journal of Biological Chemistry

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The nuclear receptor retinoid X receptor (RXR) can regulate transcription through homotetramers, homodimers, and heterodimers with other nuclear receptors such as the vitamin D receptor (VDR). The mechanisms that underlie the nuclear import of RXR, VDR, and RXR-VDR heterodimers were investigated. We show that RXR and VDR translocate into the nucleus by distinct pathways. RXR strongly bound to importin␤ and was predominantly nuclear in the absence of ligand. Importin binding and nuclear localization of RXR were modestly enhanced by its ligand, 9-cis-retinoic acid. On the other hand, VDR selectively associated with importin␣. Importin association and correspondingly nuclear import of VDR were markedly augmented by 1,25(OH) 2 D 3 . RXR-VDR dimerization inhibited the ability of RXR to bind importin␤ and to mobilize into the nucleus using its own nuclear localization signal. In contrast, VDR recruited RXR-VDR heterodimers to importin␣ and mediated nuclear import of the heterodimers in response to 1,25(OH) 2 D 3 . Hence nuclear import of RXR-VDR heterodimers is mediated preferentially by VDR and is controlled by the VDR ligand. The observations reveal a novel mechanism by which an RXR heterodimerization partner dominates the activity of the heterodimers.The retinoid X receptor (RXR) 3 is a member of the superfamily of nuclear hormone receptors that is activated by the vitamin A metabolite 9-cis-retinoic acid (9cRA). Like other nuclear receptors, RXR is comprised of several distinct functional domains: an amino-terminal domain, involved in ligand-independent basal transcriptional activity; a DNA-binding domain (DBD) containing two "zinc finger" motifs; a flexible hinge region; and a carboxyl-terminal region, termed the ligandbinding domain (LBD). The LBD contains the ligand-binding pocket as well as regions that mediate multiple protein-protein interactions including association with transcriptional co-regulators, formation of dimers, and, in the case of RXR, formation of tetramers. The LBD of nuclear receptors, including RXR, thus coordinates their liganddependent transcriptional activities (1).In the absence of its cognate ligand, RXR forms high affinity homotetramers. These tetramers are transcriptionally silent, but they rapidly dissociate upon ligand binding (2-4). Hence RXR tetramers appear to serve as an inactive storage pool from which active species can be liberated in response to 9cRA. An additional role for the RXR tetramers was recently suggested by the observations that these oligomers act as DNA architectural factors. It was thus demonstrated that binding of RXR tetramers to promoter regions that contain two RXR response elements in tandem results in a dramatic DNA looping, thereby enabling transcriptional regulation by factors placed far upstream from start sites of target genes (5). Hence by modulating DNA geometry, RXR tetramers can regulate gene expression in a manner that is responsive to 9cRA but is independent of the intrinsic transcriptional activity of the receptor (5). Although RXR can activate ...

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Section: Discussionmentioning

confidence: 99%

Nuclear Import of the Retinoid X Receptor, the Vitamin D Receptor, and Their Mutual Heterodimer

Yasmin

Williams

et al. 2005

Journal of Biological Chemistry

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“…The expanded binding repertoire of AR, including both the common IR3 and specific ADR3 elements, breaks the degeneracy of the steroid response elements, allowing specific AR activation from certain response elements but disfavoring interaction with PR, MR, or GR. This finding could further account for steroid-specific actions in vivo.The crystal structures of nuclear receptors bound to directrepeat elements, including the VDR DBD bound to a similar DR3 element, reveal a ''head-to-tail'' protein dimer bound to the DNA (6,(22)(23)(24). For AR to bind to ADR3-type elements in a head-to-tail orientation, the DBD would require a second dimerization interface that is distinct from the canonical D box region used to dimerize on IR3 elements (25).…”

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confidence: 99%

“…The crystal structures of nuclear receptors bound to directrepeat elements, including the VDR DBD bound to a similar DR3 element, reveal a ''head-to-tail'' protein dimer bound to the DNA (6,(22)(23)(24). For AR to bind to ADR3-type elements in a head-to-tail orientation, the DBD would require a second dimerization interface that is distinct from the canonical D box region used to dimerize on IR3 elements (25).…”

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confidence: 99%

Structural basis of androgen receptor binding to selective androgen response elements

Shaffer

Jivan

Dollins

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

344

336

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Steroid receptors bind as dimers to a degenerate set of response elements containing inverted repeats of a hexameric half-site separated by 3 bp of spacer (IR3). Naturally occurring selective androgen response elements have recently been identified that resemble direct repeats of the hexameric half-site (ADR3). The 3D crystal structure of the androgen receptor (AR) DNA-binding domain bound to a selective ADR3 reveals an unexpected head-tohead arrangement of the two protomers rather than the expected head-to-tail arrangement seen in nuclear receptors bound to response elements of similar geometry. Compared with the glucocorticoid receptor, the DNA-binding domain dimer interface of the AR has additional interactions that stabilize the AR dimer and increase the affinity for nonconsensus response elements. This increased interfacial stability compared with the other steroid receptors may account for the selective binding of AR to ADR3 response elements.T he androgen receptor (AR) is a ligand-activated transcription factor that plays a central role in male sexual development and in the etiology of prostate cancer (1, 2). It is a member of the steroid and nuclear hormone receptor superfamily, which also includes receptors for glucocorticoids (GR), mineralocorticoids (MR), progesterone (PR), estrogens (ER), and vitamin D (VDR) (3). Members of this family contain conserved, discrete, DNA-binding domains (DBDs) and ligand-binding domains. The amino-terminal domain and the hinge region connecting the central DBD to the C-terminal ligand-binding domain diverge among family members.The hormone receptor DBD consists of a highly conserved 66-residue core made up of two zinc-nucleated modules, shown schematically in Fig. 1 A (4, 5). With VDR as the only reported exception (6), the isolated DBD and associated C-terminal extension are necessary and sufficient to generate the same pattern of DNA response element selectivity, partner selection, and dimerization as the full-length receptor from which it is derived (6-11).Although ligand binding elicits distinct hormone-specific responses, all classical steroid receptors (AR, PR, MR, and GR) recognize identical DNA response elements, which consist of two hexameric half-sites (5Ј-AGAACA-3Ј) arranged as inverted repeats with 3 bp of separating DNA, producing the 2-fold IR3 sequence pattern (Fig. 1B) (12). A question that continues to engage the steroid receptor field is how these transcription factors achieve DNA target specificity despite this degeneracy. As seen in the structures of the GR and ER DBDs bound to IR3 elements (4, 13), the receptors bind as ''head-to-head'' homodimers whose symmetric displacement across the DNA pseudodyad reflects the underlying half-site arrangement. Differences in steroid metabolism, receptor expression, local chromatin structure, and the availability of cofactors all contribute to steroid-specific responses (14-17). However, recent work has now also identified selective androgen response elements (AREs). The AREs consist of two hexameric half-sites a...

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“…Like most nuclear receptors, RXR has two structural domains, the DNA-binding domain (DBD) and the ligand-binding domain (LBD), which are connected by a flexible hinge region. The DBD contains two zinc modules, which bind a sequence of six bases (2). The LBD binds and activates transcription in response to multiple ligands including phytanic acid, docosahexaenoic acid and 9-cis retinoic acid (9cRA) (Fig.…”

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confidence: 99%

Creation and discovery of ligand–receptor pairs for transcriptional control with small molecules

Schwimmer

Rohatgi

Azizi

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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The nuclear receptor retinoid X receptor (RXR) is a ligand-activated transcription factor. To create receptors for a new ligand, a structure-based approach was used to generate a library of Ϸ380,000 mutant RXR genes. To discover functional variants within the library, we used chemical complementation, a method of protein engineering that uses the power of genetic selection. Wild-type RXR has an EC50 of 500 nM for 9-cis retinoic acid (9cRA) and an EC50 of >10 M for the synthetic retinoid-like compound LG335 in yeast. T he human retinoid X receptor ␣ (RXR) is a ligand-activated transcription factor of the nuclear receptor superfamily. RXR plays an important role in morphogenesis and differentiation and serves as a dimerization partner for other nuclear receptors (1). Like most nuclear receptors, RXR has two structural domains, the DNA-binding domain (DBD) and the ligand-binding domain (LBD), which are connected by a flexible hinge region. The DBD contains two zinc modules, which bind a sequence of six bases (2). The LBD binds and activates transcription in response to multiple ligands including phytanic acid, docosahexaenoic acid and 9-cis retinoic acid (9cRA) (Fig. 5, which is published as supporting information on the PNAS web site) (3-6). RXR is a modular protein; the DBD and LBD function independently. Therefore, the LBD can be fused to other DBDs and retain function. A conformational change is induced in the LBD upon ligand-binding, which initiates recruitment of coactivators and the basal transcription machinery resulting in transcription of the target gene (7).Nuclear receptors have evolved to bind and activate transcription in response to a variety of small-molecule ligands. The known ligands for nuclear receptors are chemically diverse and include steroid and thyroid hormones, vitamin D, prostaglandins, fatty acids, leukotrienes, retinoids, antibiotics, and other xenobiotics. Evolutionarily closely related receptors (e.g., thyroid hormone receptor and retinoic acid receptor) bind different ligands, whereas some members of distant subfamilies (e.g., RXR and retinoic acid receptor) bind the same ligand (8). This diversity of ligand-receptor interactions demonstrates the versatility of the fold for ligandbinding and suggests that it should be possible to engineer LBDs with a large range of novel specificities.The crystal structure of RXR bound to 9cRA elucidates important hydrophobic and polar interactions in the LBD binding pocket (9). There are 20 hydrophobic and polar amino acids within 4.4 Å of the bound 9cRA (Fig. 6, which is published as supporting information on the PNAS web site). RXR is a good candidate for creating variants that bind different ligands through site-directed mutagenesis, because side-chain atoms, not main-chain atoms, contribute the majority of the ligand contacts (10-13). A library of RXR LBDs with all 20 amino acids at each of the 20 positions in the ligand-binding pocket screened against multiple compounds could potentially produce many new ligand-receptor pairs. However, the numb...

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Structural basis of RXR-DNA interactions 1 1Edited by P. E. Wright

Cited by 126 publications

References 51 publications

Nuclear Import of the Retinoid X Receptor, the Vitamin D Receptor, and Their Mutual Heterodimer

Nuclear Import of the Retinoid X Receptor, the Vitamin D Receptor, and Their Mutual Heterodimer

Structural basis of androgen receptor binding to selective androgen response elements

Creation and discovery of ligand–receptor pairs for transcriptional control with small molecules

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