Journal of Molecular Biology
Regular articleHigh-resolution solution structure of the retinoid X receptor DNA-binding domaina
Introduction
The retinoid X receptor, RXRα, is a central member of the nuclear hormone receptor superfamily of ligand-controlled transcription factors (Mangelsdorf & Evans, 1995). These receptors activate and repress gene expression by binding cooperatively as dimers to hormone response elements composed of two copies of a six nucleotide motif. RXRα recognizes the consensus half-site sequence AGGTCA Mangelsdorf et al 1990, Naar et al 1991. While a subset of the receptors, including the estrogen and glucocorticoid receptors (ER and GR), bind to half-site sequences arranged as inverted repeats, forming symmetric protein-protein dimers, the RXRα half-sites are arranged as direct repeats such that the protein must dimerize in a head-to-tail fashion (Mangelsdorf et al., 1995). Like other members of the superfamily, RXRα transactivates as a homodimer in response to binding of its activating ligand, 9-cis- retinoic acid Zhang et al 1992b, Mangelsdorf et al 1991. However, RXRα also regulates transcription by forming heterodimers with a number of other nuclear hormone receptors, including the thyroid receptor (TR), retinoic acid receptor (RAR), vitamin D receptor (VDR), and peroxisome proliferator-activated receptor (PPAR;Leid et al 1992, Yu et al 1991, Kliewer et al 1992a, Kliewer et al 1992b, Zhang et al 1992a, Bugge et al 1992). Selective recognition of the hormone response elements by the various heterodimers is encoded, in part, by variable spacing between the half-site repeats. RXRα heterodimers with PPAR, VDR, TR and RAR transactivate through response elements with one, three, four or five base-pairs between half-sites, respectively (Umesono et al., 1991).
The DNA-binding function of the receptor is located in an approximately 70 amino acid residue domain, which has a high degree of homology within the hormone receptor superfamily and includes nine conserved cysteine residues (Mangelsdorf et al., 1990). The structure of this DNA-binding domain (DBD) has been determined for ER Schwabe et al 1990, Schwabe et al 1993, GR Luisi et al 1991, Hard et al 1990, Van Tilborg et al 1995, Baumann et al 1993, RAR (Knegtel et al., 1993), TR (Rastinejad et al., 1995) and RXRα Lee et al 1993, Rastinejad et al 1995. The general characteristics of the DBD structures are that eight cysteine residues tetrahedrally coordinate two zinc ions forming two “loop-helix” zinc finger domains. The two helices of the zinc fingers pack perpendicularly to each other, forming a globular domain held together by hydrophobic side-chains that pack into the hydrophobic core.
A low-resolution structure of the RXRα DBD was initially determined in solution by NMR spectroscopy (Lee et al., 1993). Subsequently, a crystal structure of the RXRα DBD-TR DBD heterodimeric complex bound to a hormone response element with a four base-pair spacing (DR4) was determined (Rastinejad et al., 1995). The solution structure revealed an overall fold for the zinc finger domains similar to that of other nuclear hormone receptor and steroid receptor DBDs. At the C terminus, however, an additional helix (residues 202 to 209, seeFigure 1) was observed that has not been found in other DBD structures. This novel helix follows the conserved Gly-Met sequence and is formed by residues that are part of the “T-box”, a region that has been shown to play a key role in homodimeric binding to a hormone response element with a one base-pair spacing between half-sites (DR1;Wilson et al 1992, Lee et al 1993). Interestingly, this additional helix was not seen in the crystal structure of the heterodimer-DNA complex; no electron density was observed for this region of the protein (Rastinejad et al., 1995).
Here, we report the calculation of a high-resolution NMR structure of the RXRα DBD as a monomer in solution. The results unequivocally confirm the existence of the C-terminal helix in free RXRα. The improved structural definition allows a more detailed comparison of the free and DNA-bound states of the RXRα DBD, giving a better understanding of the structural changes that might occur as a consequence of dimerization and DNA-binding. Important questions remain about the nature of the cooperative binding of RXR to DNA, such as whether or not it involves local folding of the RXRα on the DNA and how RXRα accommodates such a variety of partners and response elements. We compare our structure to the RXRα-TR crystal structure to obtain some insight into these questions for RXRα on DR4. We also model the RXRα homodimer on DR1 to attempt to understand the role of the third helix in homodimer formation.
Section snippets
Design of expression construct
The construct used for the low-resolution structure (Lee et al., 1993) consisted of RXRα residues 130 to 229 and contained all nine of the conserved cysteine residues. This protein had a tendency to precipitate and, as a result, the maximum sample concentration for NMR studies was approximately 0.6 mM. It was suspected that cysteine 195, which neither coordinates zinc nor participates in an intramolecular disulfide linkage, might be causing precipitation through oxidative dimerization. The
Conclusions
The high-resolution solution structure of RXRα DBD has allowed a detailed comparison of the free and DNA-bound states of the protein. Two important structural features are revealed, both involved in formation of the dimer interface. The first is the presence of a C-terminal helix, which is well ordered at its N terminus as a consequence of packing interactions with the hydrophobic core but is frayed over the last four or five residues. Modeling of the RXRα homodimer on DNA suggests that the
Construction of C195A
In order to prevent oxidative dimerization of the RXRα DBD, the non-coordinating Cys195 was substituted with an alanine following an established PCR-based mutagenesis procedure (Higuchi et al., 1988) and using the fusion GST-RXRα(130-223) expression plasmid Lee et al 1993, Lee et al 1994 as a template. The following primers were designed to incorporate the mutation (underlined): 5′-GCCGCTACCAGAAGCTGGCCATGGG-3′ and 3′-GCGATGGTCTTCGACCGGTACCCG-5′.
The mutated gene was amplified using two
Acknowledgements
We thank David Case, Ishwar Radhakrishnan, John Love, Jarrod Smith, Tom Macke, Debbie Wuttke and Shohei Koide for helpful discussions; Xiang Li for making available the XPKASGN program; John Chung for assistance with NMR experiments; and Linda Tennant and Martine Reymond for technical assistance. This work was supported by grant GM36643 from the National Institutes of Health. S.M.A.H. and M.P.F. are recipients of American Cancer Society Fellowships.
References (60)
- et al.
An alternative 3D NMR technique for correlating backbone 15N with side-chain Hβ resonances in larger proteins
J. Magn. Reson.
(1991) - et al.
1H-1H correlation via isotropic mixing of 13C magnetization, a new three-dimensional approach for assigning 1H and 13C spectra of 13C-enriched proteins
J. Magn. Reson.
(1990) - et al.
An efficient experiment for sequential backbone assignment of medium-sized isotopically enriched proteins
J. Magn. Reson.
(1992) - et al.
Correlation of backbone amide and aliphatic side-chain resonances in 13C/15N-enriched proteins by isotropic mixing of 13C magnetization
J. Magn. Reson. ser. B
(1993) - et al.
Structure determination of the Antp (C39→S) homeodomain from nuclear magnetic resonance data in solution using a novel strategy for the structure calculation with the programs DIANA, CALIBA, HABAS and GLOMSA
J. Mol. Biol.
(1991) - et al.
Purification, cloning, and RXR identity of the HeLA cell factor with which RAR or TR heterodimerizes to bind target sequences efficiently
Cell
(1992) - et al.
The RXR heterodimers and orphan receptors
Cell
(1995) - et al.
A direct repeat in the cellular retinol-binding protein type II gene confers differential regulation by RXR and RAR
Cell
(1991) - et al.
The nuclear receptor superfamily: the second decade
Cell
(1995) - et al.
Solvent suppression using a spin lock in 2D and 3D NMR spectroscopy with H2O solutions
J. Magn. Reson.
(1989)
The orientation and spacing of core DNA-binding motifs dictate selective transcriptional responses to three nuclear hormone receptors
Cell
Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities
J. Mol. Biol.
The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements
Cell
NMR spectroscopic studies of the DNA-binding domain of the monomer-binding nuclear orphan receptor, human estrogen related receptor. 2. The carboxyl-terminal extension to the zinc-finger region is unstructured in the free form of the protein
J. Biol. Chem.
Direct repeats as selective response elements for the thyroid hormone, retinoic acid, and vitamin D3receptors
Cell
Structure refinement of the glucocorticoid receptor-DNA-binding domain from NMR data by relaxation matrix calculations
J. Mol. Biol.
RXRβa coregulator that enhances binding of retinoic acid, thyroid hormone, and vitamin D receptors to their cognate response elements
Cell
Refined solution structure of the glucocorticoid receptor DNA-binding domain
Biochemistry
Backbone dynamics of the glucocorticoid receptor DNA-binding domain
Biochemistry
RXRα, a promiscuous partner of retinoic acid and thyroid hormone receptors
EMBO J.
Backbone dynamics of a free and a phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation
Biochemistry
Correlating backbone amide and side-chain resonances in larger proteins by multiple relayed triple resonance NMR
J. Am. Chem. Soc.
Amino acid type determination in the sequential assignment procedure of uniformly 13C/15N-enriched proteins
J. Biomol. NMR
A simple and sensitive experiment for measurement of JCCcouplings between backbone carbonyl and methyl carbons in isotopically enriched proteins
J. Biomol. NMR
Multiple-quantum line narrowing for measurement of Hα-HβJ coupling in isotopically enriched proteins
J. Am. Chem. Soc.
Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints
J. Biomol. NMR
Solution structure of the glucocorticoid receptor DNA-binding domain
Science
A general method of in vitro preparation and specific mutagenesis of DNA fragments: study of protein and DNA interactions
Nucl. Acids Res.
HERA - a program to draw schematic diagrams of protein secondary structures
Proteins: Struct. Funct. Genet.
PROMOTIF-a program to identify and analyze structural motifs in proteins
Protein Sci.
Cited by (0)
- a
Edited by F. Cohen