Structural elements of an orphan nuclear receptor-DNA complex

Molecular Cell

Volumn 1, Issue 6, 1998, Pages 849-861

  Zhao, Qiang ^a   Khorasanizadeh, Sepideh ^a   Miyoshi, Yoji ^b   Lazar, Mitchell A ^b   Rastinejad, Fraydoon ^a  

^a UNIVERSITY OF VIRGINIA   (United States)

^b HOSPITAL OF THE UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL RECEPTOR; DNA; DNA BINDING PROTEIN; NR1D1 PROTEIN, HUMAN; NUCLEAR PROTEIN; PROTEIN; STEROID RECEPTOR;

ARTICLE; BINDING SITE; CHEMISTRY; CONFORMATION; CRYSTALLOGRAPHY; GENETICS; HUMAN; IMAGE PROCESSING; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY;

BINDING SITES; CONSERVED SEQUENCE; CRYSTALLOGRAPHY; DNA; DNA-BINDING PROTEINS; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; MOLECULAR SEQUENCE DATA; NUCLEAR PROTEINS; NUCLEIC ACID CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; RECEPTORS, CYTOPLASMIC AND NUCLEAR; RECEPTORS, STEROID; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 0032059865     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1097-2765(00)80084-2     Document Type: Article

References (66)

1. Adams, P.D., Pannu, N.S., Read, R.J., and Brünger, A.T. (1997). Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement. Proc. Natl. Acad. Sci. USA 94, 5018-5023.
2. Baes, M., Gulick, T., Choi, H.S., Martinoli, M.G., Simha, D., and Moore, D.D. (1994). A new orphan member of the nuclear hormone receptor superfamily that interacts with a subset of retinoic acid response elements. Mol. Cell. Biol. 14, 1544-1551.
3. Bilder, D.W., and Scott, M.P. (1995). Genomic regions required for morphogenesis of the Drosophila embryonic midgut. Genomics 14, 1087-1100.
4. Brünger, A.T. (1992). X-PLOR Manual Version 3.1 (New Haven, CT: Yale University Press).
5. Carlberg, C., HooftvanHuijsduijnen, R., Staple, J.K., DeLamarter, J.F., and Becker-Andre, M. (1994). RZRs, a new family of retinoid-related orphan receptors that function as both monomers and homodimers. Mol. Endocrinol. 8, 757-770.
6. Chawla, A., and Lazar, M.A. (1993). Induction of Rev-ErbAa, an orphan nuclear receptor encoded on the opposite strand of the α-thyroid hormone receptor gene, during adipocyte differentiation. J. Biol. Chem. 268, 16265-16269.
7. Devchand, P.R., Keller, H., Peters, J.M., Vazquez, M., Gonzalez, F.J., and Wahli, W. (1996). The PPARa-leukotriene B4 pathway to inflammation control. Nature 384, 39-43.
8. DiRenzo, J., Soderstrom, M., Kurokawa, R., Ogliastro, M.H., Ricote, M., Ingrey, S., Horlein, A., Rosenfeld, M.G., and Glass, C.K. (1997). Peroxisome proliferator-activated receptors and retinoicacid receptors differentially control the interactions of retinoid X receptor heterodimers with ligands, coactivators, and corepressors. Mol. Cell. Biol. 17, 2166-2176.
9. Downes, M., Carozzi, A.J., and Muscat, G.E. (1995). Constitutive expression of the orphan receptor, Rev-ErbAα, inhibits muscle differentiation and abrogates the expression of the myoD gene family. Mol. Endocrinol. 9, 1666-1678.
10. Dumas, B., Harding, H., Choi, H.-S., Lehmann, K., Chung, M., Lazar, M.A., and Moore, D.D. (1994). A new orphan member of the nuclear hormone receptor superfamily closely related to Rev-Erb. Mol. Endocrinol. 8, 996-1005.
11. Enmark, E., and Gustafsson, J.-A. (1996). Orphan nuclear receptors - the first eight years. Mol. Endocrinol. 10, 1293-1307.
12. Forman, B.M., Chen, J., Blumberg, B., Kliewer, S.A., Henshaw, R., Ong, E.S., and Evans, R.M. (1994). Cross-talk among RORα1 and the Rev-erb family of orphan nuclear receptors. Mol. Endocrinol. 8, 1253-1261.
13. Forman, B.M., Chen, J., and Evans, R.M. (1997). Hypolipidemic drugs, polyunsaturated fatty acids, and eicosanoids are ligands for peroxisome proliferator-activated receptors α and δ. Proc. Natl. Acad. Sci. USA 94, 4312-4317.
14. Forman, B.M., Tontonoz, P., Chen, J., Brun, R.P., Spiegelman, B.M., and Evans, R.M. (1995a). 15-deoxy, delta 12, 14-prostaglandin J2 is a ligand for the adipocyte determination factor PPARγ. Cell 83, 803-812.
15. Forman, B.M., Umesono, K., Chen, J., and Evans, R.M. (1995b). Unique response pathways are established by allosteric interactions among nuclear hormone receptors. Cell 81, 541-550.
16. Giguere, V., McBroom, L.D.B., and Flock, G. (1995). Determinants of target gene specificity for RORα: monomeric DNA binding by an orphan nuclear receptor. Mol. Cell. Biol. 15, 2517-2526.
17. Giguere, V., Tini, M., Flock, G., Ong, E., Evans, R.M., and Otulakowski, G. (1994). Isoform-specific amino-terminal domains dictate DNA-binding properties of RORα, a novel family of orphan hormone nuclear receptors. Genes Dev. 8, 538-553.
18. Glass, C.K., Rose, D.W., and Rosenfeld, M.G. (1997). Nuclear receptor coactivators. Curr. Opin. Cell. Biol. 9, 222-232.
19. Harding, H.P. (1995). DNA binding and transcriptional regulation by the orphan receptor Rev-Erb. In Molecular Biology (Philadelphia: University of Pennsylvania).
20. Harding, H.P., and Lazar, M.A. (1995).The monomer-binding orphan receptor Rev-Erb represses transcription as a dimer on a novel direct repeat. Mol. Cell. Biol. 15, 4791-4802.
21. Harding, H.P., and Lazar, M.A. (1993). The orphan receptor Rev-ErbAa activates transcription via a novel response element. Mol. Cell. Biol. 13, 3113-3121.
22. Harding, H.P., Atkins, G.B., Jaffe, A.G., Seo, W.J., and Lazar, M.A. (1997). Transcriptional activation and repression by RORα, an orphan nuclear receptor required for cerebellar development. Mol. Endocrinol. 11, 1737-1746.
23. Horwitz, K.B., Jackson, T.A., Bain, D.L., Richer, J.K., Takimoto, G.S., and Tung, L. (1996). Nuclear receptor coactivators and corepressors. Mol. Endocrinol. 10, 1167-1177.
24. Huth, J.R., Bewley, C.A., Nissen, M.S., Evans, J.N.S., Reeves, R., Gronenborn, A.M., and Clore, G.M. (1997). The solution structure of an HMG-1(Y)-DNA complex defines a new architectural minor groove binding motif. Nat. Struct. Biol. 4, 657-665.
25. Ijpenberg, A., Jeannin, E., Wahli, W., and Desvergne, B. (1997). Polarity and specific sequence requirements of peroxisome proliferator-activated receptor (PPAR)/retinoid X receptor heterodimer binding to DNA. J. Biol. Chem. 272, 20108-20117.
26. Jiang, G., Nepomuceno, L., Hopkins, K., and Sladek, F. (1995). Exclusive homodimerization of the orphan receptor hepatocyte nuclear factor 4 defines a new subclass of nuclear receptors. Mol. Cell. Biol. 15, 5131-5143.
27. Jones, T.A., Zou, J.Y., Cowan, S.W., and Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst. 47, 110-119.
28. Juge-Aubry, C., Pernin, A., Favez, T., Burger, A.G., Wahli, W., Meier, C.A., and Desvergne, B. (1997). DNA binding properties of peroxisome proliferator-activated receptor on various natural peroxisome proliferator response elements. Importance of the5′-flanking region. J. Biol. Chem. 272, 25252-25259.
29. Katz, R.W., and Koenig, R.J. (1993). Nonbiased identification of DNA sequences that bind thyroid hormone receptor alpha 1 with high affinity. J. Biol. Chem. 268, 19392-19397.
30. Kliewer, S.A., Lenhard, J.M., Willson, T.M., Patel, I., Morris, D.C., and Lehmann, J.M. (1995). A prostaglandin J2 metabolite binds peroxisome proliferator-activated receptor γ and promotes adipocyte differentiation. Cell 83, 813-819.
31. Kliewer, S.A., Sundeth, S.S., Jones, S.A., Brown, P.J., Wisely, G.B., Koble, C.S., Devchand, P., Wahli, W., Willson, T.M., Lenhard, J.M., and Lehmann, J.M. (1997). Fatty acids and eicosanoids regulate gene expression through direct interactions with peroxisome proliferator-activated receptors α and γ. Proc. Natl. Acad. Sci. USA 94, 4318-4323.
32. Kraulis, P.J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of proteins. J. Appl. Cryst. 24, 946-950.
33. Lazar, M.A., and Harding, H.P. (1997). Monomeric nuclear receptors. In Molecular Biology of Steroid and Nuclear Hormone Receptors, L.P. Freedman, ed. (Cambridge: Birkhauser Boston).
34. Lazar, M.A., Hodin, R.A., Darling, D.S., and Chin, W.W. (1989). A novel member of the thyroid/steroid hormone receptor family is encoded by the opposite strand of the rat c-erbA α transcriptional unit. Mol. Cell. Biol. 9, 1128-1136.
35. Lehmann, J.M., Moore, L.B., Smith-Oliver, T.A., Wilkison, W.O., Willson, T.M., and Kliewer, S.A. (1995). An antidiabetic thiazolidinedione is a high affinity ligand for the nuclear peroxisome proliferator-activated receptor γ (PPARγ). J. Biol. Chem. 270, 12953-12956.
36. Luisi, B.F., Xu, W.X., Otwinowski, Z., Freedman, L.P., Yamamoto, K.R., and Sigler, P.B. (1991 ). Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. Nature 352, 497-505.
37. Mader, S., Chen, J.Y., Chen, Z., White, J., Chambon, P., and Gronemeyer, H. (1993). The patterns of binding of RAR, RXR, and TR homo- and heterodimers to direct repeats are dictated by the binding specificities of the DNA binding domains. EMBO J. 12, 5029-5041.
38. Mangelsdorf, D.J., and Evans, R.M. (1995). The RXR heterodimers and orphan receptors. Cell 83, 841-850.
39. Mangelsdorf, D.J., Thummel, C., Beato, M., Herrlich, P., Schutz, G., Umesono, K., Blumberg, B., Kastner, P., Mark, M., Chambon, P., and Evans, R.M. (1995). The nuclear receptor superfamly: the second decade. Cell 83, 835-839.
40. McBroom, L.D.B., Flock, G., and Giguere, V. (1995). The nonconserved hinge region and distinct amino-terminal domains of the RORα orphan nuclear receptor isoforms are required for proper DNA bending and RORα-DNA interactions. Mol. Cell. Biol. 15, 796-808.
41. Merritt, E.A., and Murphy, M.E.P. (1994). Paster3D version 2.0. A program for photorealistic molecular graphics. Acta Cryst. 50, 869-873.
42. Miyajima, N., Horiuchi, R., Shibuya, Y., Fukushige, S., Matsubara, K., Toyoshima, K., and Yamamoto, T. (1989). Two erbA homologs encoding proteins with different T3 binding capacities are transcribed from opposite DNA strands of the same genetic locus. Cell 57, 31-39.
43. Navaza, J. (1994). AMORE: an automated package for molecular replacement. Acta Cryst. A450, 157-163.
44. Nicholls, A., Sharp, K.A., and Honig, B. (1991). Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281-296.
45. O'Malley, B.W., and Conneely, O.M. (1992). Orphan receptors: in search of a unifying hypothesis for activation. Mol. Endocrinol. 6, 1359-1361.
46. Otwinowski, Z., and Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. Meth. Enzymol. 276, 307-326.
47. Palmer, C.N.A., Hsu, M.-H., Griffin, K.J., and Johnson, E.F. (1995). Novel sequence determinants in peroxisome proliferator signaling. J. Biol. Chem. 270, 16114-16121.
48. Perlmann, T., and Jansson, L. (1995). A novel pathway for vitamin A signaling mediated by RXR heterodimerization with NGFI-B and NURR1. Genes Dev. 9, 769-782.
49. Perlmann, T., Rangarajan, P.N., Umesono, K., and Evans, R.M. (1993). Determinants for selective RAR and TR recognition of direct repeat HREs. Genes Dev. 7, 1411-1422.
50. Rastinejad, F., Perlmann, T., Evans, R.M., and Sigler, P.B. (1995). Structural determinants of nuclear receptor assembly on DNA direct repeats. Nature 375, 203-211.
51. Retnakaran, R., Flock, G., and Giguere, V. (1994). Identification of RVR, a novel orphan nuclear receptor that acts as a negative transcriptional regulator. Mol. Endocrinol. 8, 1234-1244.
52. Schwabe, J.W., Chapman, L., Finch, J.T., and Rhodes, D. (1993). The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate among their response elements. Cell 75, 567-578.
53. Segraves, W.A., and Hogness, D.S. (1990). The E75 ecdysone-inducible gene responsible for the 75B early puff in Drosophila encodes two new members of the steroid receptor superfamily. Genes Dev. 4, 204-219.
54. Stunnenberg, H.G. (1993). Mechanisms of transactivation by retinoic acid receptors. BioEssays 15, 309-315.
55. Terenzi, H., Cassio, R.O., and Zakin, M. (1996). Expression, purification, and functional analysis of the DNA binding domain of the nuclear receptor Rev-Erbβ. Prot. Expr. Purif. 8, 313-318.
56. Tickle, I.J., and Driessen, H.P.C. (1996). Molecular replacement using known structural information. In Crystallographic Methods and Protocols, C. Jones, B. Mulloy, and M. Sanderson, eds. (Totowa, NJ: Humana Press, Inc.), pp. 173-201.
57. Ueda, H., Sun, G.C., Murata, T., and Hirose, S. (1992). A novel DNA-binding motif abuts the zinc finger domain of insect nuclear hormone receptor FTZ-F1 and mouse embryonal long terminal repeat-binding protein. Mol. Cell. Biol. 12, 5667-5672.
58. Umesono, K., Murakami, K.K., Thompson, C.C., and Evans, R.M. (1991). Direct repeats as selective response elements forthe thyroid hormone, retinoic acid, and vitamin D3 receptors. Cell 65, 1255-1266.
59. White, K.P., Hurban, P., Watanabe, T., and Hogness, D.S. (1997). Coordination of Drosophila metamorphosis by two ecdysone-induced nuclear receptors. Science 276, 114-117.
60. Willy, P.J., Umesono, K., Ong, E.S., Evans, R.M., Heyman, R.A., and Mangelsdorf, D.J. (1995). LXR, a nuclear receptor that defines a distinct retinoid response pathway. Genes Dev. 9, 1033-1045.
61. Wilson, T.E., Fahrner, T.J., and Milbrandt, J. (1993a). The orphan receptors NGFI-B and steroidogenic factor 1 establish monomer binding as a third paradigm of nuclear receptor-DNA interaction. Mol. Cell. Biol. 13, 5794-5804.
62. Wilson, T.E., Mouw, A.R., Weaver, C.A., Milbrandt, J., and Parker, K.L. (1993b). The orphan nuclear receptor NGFI-B regulates expression of the gene encoding steroid 21-hydroxylase. Mol. Cell. Biol. 13, 861-868.
63. Wilson, T.E., Paulsen, R.E., Padgett, K.A., and Milbrandt, J. (1992). Participation of non-zinc finger residues in DNA binding by two nuclear orphan receptors. Science 256, 107-110.
64. Yu, K., Bayona, W., Kallen, C.B., Harding, H.P., Ravera, C., McMahon, J., Brown, M., and Lazar, M.A. (1995). Differential activation of peroxisome proliferator-activated receptors by eicosanoids. J. Biol. Chem. 270, 23975-23983.
65. Zamir, I., Harding, H.P., Atkins, G.B., Horlein, A., Glass, C.K., Rosenfeld, M.G., and Lazar, M.A. (1996). A nuclear hormone receptor corepressor mediates transcriptional silencing by receptors with different repression domains. Mol. Cell. Biol. 16, 5458-5465.
66. Zamir, I., Zhang, J., and Lazar, M.A. (1997). Stoichiometric and steric principles governing repression by nuclear hormone receptors. Genes Dev. 11, 835-846.