Architecture of DNA bound RAR heterodimers

Sub-Cellular Biochemistry

Volumn 70, Issue , 2014, Pages 21-36

  Rochel, Natacha ^a   Moras, Dino ^a  

^a UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ISOPROTEIN; LIGAND; RETINOIC ACID; RETINOIC ACID RECEPTOR; RETINOID X RECEPTOR; RETINOL;

CHEMICAL STRUCTURE; CHEMISTRY; DNA RESPONSIVE ELEMENT; GENE EXPRESSION REGULATION; GENETICS; HUMAN; METABOLISM; PROTEIN BINDING; PROTEIN MULTIMERIZATION; PROTEIN TERTIARY STRUCTURE; REVIEW; SIGNAL TRANSDUCTION;

GENE EXPRESSION REGULATION; HUMANS; LIGANDS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN ISOFORMS; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, TERTIARY; RECEPTORS, RETINOIC ACID; RESPONSE ELEMENTS; RETINOID X RECEPTORS; SIGNAL TRANSDUCTION; TRETINOIN; VITAMIN A;

EID: 84910118219     PISSN: 03060225     EISSN: None     Source Type: Journal    
DOI: 10.1007/978-94-017-9050-5_2     Document Type: Article

References (61)

1. Aoyagi S, Archer TK (2008) Dynamics of coactivator recruitment and chromatin modifications during nuclear receptor mediated transcription. Mol Cell Endo 280:1-5
2. Balmer JE, Blomhoff R (2005) A robust characterization of retinoic acid response elements based on a comparison of sites in three species. J Steroid Biochem Mol Biol 96:347-354
3. Berger I, Blanco AG, Boelens R, Cavarelli J, Coll M, Folkers GE, Nie Y, Pogenberg V, Schultz P, Wilmanns M, Moras D, Poterszman A (2011) Structural insights into transcription complexes. J Struct Biol 175:135-146
4. Billas I, Moras D (2013) Allosteric controls of nuclear receptor function in the regulation of transcription. J Mol Biol 425:2317-2329
5. Bourguet W, Ruff M, Chambon P, Gronemeyer H, Moras D (1995) Crystal structure of the ligand-binding domain of the human nuclear receptor RXR-alpha. Nature 375:377-382
6. Bourguet W, Vivat V, Wurtz JM, Chambon P, Gronemeyer H, Moras D (2000) Crystal structure of a heterodimeric complex of RAR and RXR ligand-binding domains. Mol Cell 5:289-298
7. Chandra V, Huang P, Hamuro Y, Raghuram S, Wang Y, Burris TP, Rastinejad F (2008) Structure of the intact PPAR-gamma-RXR- nuclear receptor complex on DNA. Nature 456:350-356
8. Chandra V, Huang P, Potluri N, Wu D, Kim Y, Rastinejad F (2013) Multidomain integration in the structure of the HNF-4alpha nuclear receptor complex. Nature 495:394-398
9. Cramer P, Bushnell DA, Kornberg RD (2001) Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292:1863-1876
10. Deisenhofer J, Epp O, Miki K, Huber R, Michel H (1984) X-ray structure analysis of a membrane protein complex. Electron density map at 3 A resolution and a model of the chromophores of the photosynthetic reaction center from Rhodopseudomonas viridis. J Mol Biol 180:385-398
11. Delacroix L, Moutier E, Altobelli G, Legras S, Poch O, Choukrallah MA, Bertin I, Jost B, Davidson I (2010) Cell-specific interaction of retinoic acid receptors with target genes in mouse embryonic fibroblasts and embryonic stem cells. Mol Cell Biol 30:231-244
12. Egea PF, Mitschler A, Rochel N, Ruff M, Chambon P, Moras D (2000) Crystal structure of the human RXRalpha ligand-binding domain bound to its natural ligand: 9-cis retinoic acid. EMBO J 19:2592-2601
13. Germain P, Iyer J, Zechel C, Gronemeyer H (2002) Co-regulator recruitment and the mechanism of retinoic acid receptor synergy. Nature 415:187-192
14. Gherardi E, Sandin S, Petoukhov MV, Finch J, Youles ME, Ofverstedt LG, Miguel RN, Blundell TL, Vande Woude GF, Skoglund U, Svergun DI (2006) Structural basis of hepatocyte growth factor/scatter factor and MET signalling. Proc Natl Acad Sci USA 103:4046-4051
15. Glass CK, Rosenfeld MG (2000) The coregulator exchange in transcriptional functions of nuclear receptors. Genes Dev 14:121-141
16. Hammel M (2012) Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS). Eur Biophys J 41:789-799
17. Helsen C, Claessens F (2013) Looking at nuclear receptors from a new angle. Mol Cell Endocrinol 382:97-106
18. Hua S, Kittler R, White KP (2009) Genomic antagonism between retinoic acid and estrogen signaling in breast cancer. Cell 137:1259-1271
19. Jin L, Li Y (2010) Structural and functional insights into nuclear receptor signaling. Adv Drug Deliv Rev 62:1218-1226
20. Kersten S, Dawson MI, Lewis BA, Noy N (1996) Individual subunits of heterodimers comprised of retinoic acid and retinoid X receptors interact with their ligands independently. Biochemistry 35:3816-3824
21. Kim SH, Suddath FL, Quigley GJ, McPherson A, Sussman JL, Wang AH, Seeman NC, Rich A (1974) Three-dimensional structure of yeast phenylalanine transfer RNA. Science 185:435-440
22. Konermann L, Pan J, Liu YH (2011) Hydrogen exchange mass spectrometry for studying protein structure and dynamics. Chem Soc Rev 40:1224-1234
23. Lala DS, Mukherjee R, Schulman IG, Koch SS, Dardashti LJ, Nadzan AM, Croston GE, Evans RM, Heyman RA (1996) Activation of specific RXR heterodimers by an antagonist of RXR homodimers. Nature 383:450-453
24. le Maire A, Teyssier C, Erb C, Grimaldi M, Alvarez S, de Lera AR, Balaguer P, Gronemeyer H, Royer CA, Germain P, Bourguet W (2010) A unique secondary-structure switch controls constitutive gene repression by retinoic acid receptor. Nat Struct Mol Biol 17:801-807
25. Lonard DM, O'Malley BW (2012) Nuclear receptor coregulators: modulators of pathology and therapeutic targets. Nat Rev Endocrinol 8:598-604
26. Luisi BF, Xu WX, Otwinowski Z, Freedman LP, Yamamoto KR, Sigler PB (1991) Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. Nature 352:497-505
27. Mader S, Chen JY, Chen Z, White J, Chambon P, Gronemeyer H (1993) The patterns of binding of RAR, RXR and TR homo- and heterodimers to direct repeats are dictated by the binding specificites of the DNA binding domains. EMBO J 12:5029-5041
28. Martens JH, Brinkman AB, Simmer F, Francoijs KJ, Nebbioso A, Ferrara F, Altucci L, Stunnenberg HG (2010) PML-RARalpha/RXR Alters the Epigenetic Landscape in Acute Promyelocytic Leukemia. Cancer Cell 17:173-185
29. Martens JH, Rao NA, Stunnenberg HG (2011) Genome-wide interplay of nuclear receptors with the epigenome. Biochim Biophys Acta 1812:818-823
30. McEwan IJ (2012) Nuclear hormone receptors: allosteric switches. Mol Cell Endocrinol 348:345-347
31. McEwan IJ, Lavery D, Fischer K, Watt K (2007) Natural disordered sequences in the amino terminal domain of nuclear receptors: lessons from the androgen and glucocorticoid receptors. Nucl Recept Signal 5:e001
32. Meijsing SH, Pufall MA, So AY, Bates DL, Chen L, Yamamoto KR (2009) DNA binding site sequence directs glucocorticoid receptor structure and activity. Science 324:407-410
33. Moutier E, Ye T, Choukrallah MA, Urban S, Osz J, Chatagnon A, Delacroix L, Langer D, Rochel N, Moras D, Benoit G, Davidson I (2012) Retinoic acid receptors recognize the mouse genome through binding elements with diverse spacing and topology. J Biol Chem 287:26328-26341
34. Nagy L, Kao HY, Love JD, Li C, Banayo E, Gooch JT, Krishna V, Chatterjee K, Evans RM, Schwabe JW (1999) Mechanism of corepressor binding and release from nuclear hormone receptors. Genes Dev 13:3209-3216
35. Nolte RT, Wisely GB, Westin S, Cobb JE, Lambert MH, Kurokawa R, Rosenfeld MG, Willson TM, Glass CK, Milburn MV (1998) Ligand binding and co-activator assembly of the peroxisome proliferator-activated receptor-gamma. Nature 95:137-143
36. Orlov I, Rochel N, Moras D, Klaholz BP (2012) Structure of the full human RXR/VDR nuclear receptor heterodimer complex with its DR3 target DNA. EMBO J 31:291-300
37. Osz J, Pethoukhov MV, Sirigu S, Svergun DI, Moras D, Rochel N (2012) Solution structures of PPARgamma2/RXRalpha complexes. PPAR Res 701412
38. Osz J, Brélivet Y, Peluso-Iltis C, Cura V, Eiler S, Ruff M, Bourguet W, Rochel N, Moras D (2012) Structural basis for a molecular allosteric control mechanism of cofactor binding to nuclear receptors. Proc Natl Acad Sci USA 109:E588-E594
39. Pawlak M, Lefebvre P, Staels B (2012) General molecular biology and architecture of nuclear receptors. Curr Top Med Chem 12:486-504
40. Perissi V, Rosenfeld MG (2005) Controlling nuclear receptors: the circular logic of cofactor cycles. Nat Rev Mol Cell Biol 6:542-554
41. Perlmann T, Rangarajan PN, Umesono K, Evans RM (1993) Determinants for selective RAR and TR recognition of direct repeat HREs. Genes Dev 7:1411-1422
42. Pogenberg V, Guichou JF, Vivat-Hannah V, Kammerer S, Pérez E, Germain P, de Lera AR, Gronemeyer H, Royer CA, Bourguet W (2005) Characterization of the interaction between retinoic acid receptor/retinoid X receptor (RAR/RXR) heterodimers and transcriptional coactivators through structural and fluorescence anisotropy studies. J Biol Chem 280:1625-1633
43. Putcha BD, Fernandez EJ (2009) Direct interdomain interactions can mediate allosterism in the thyroid receptor. J Biol Chem 284:22517-22524
44. Rambo RP, Tainer JA (2013) Super-resolution in solution x-ray scattering and its applications to structural systems biology. Annu Rev Biophys. 42:415-441
45. Rastinejad F, Wagner T, Zhao Q, Khorasanizadeh S (2000) Structure of the RXR-RAR DNAbinding complex on the retinoic acid response element DR1. EMBO J 19:1045-1054
46. Renaud JP, Rochel N, Ruff M, Vivat V, Chambon P, Gronemeyer H, Moras D (1995) Crystal structure of the RAR-gamma ligand-binding domain bound to all-trans retinoic acid. Nature 378:681-689
47. Robertus JD, Ladner JE, Finch JT, Rhodes D, Brown RS, Clark BF, Klug A (1974) Structure of yeast phenylalanine tRNA at 3 A resolution. Nature 250:546-551
48. Rochel N, Ciesielski F, Godet J, Moman E, Roessle M, Peluso-Iltis C, Moulin M, Haertlein M, Callow P, Mély Y, Svergun DI, Moras D (2011) Common architecture of nuclear receptor heterodimers on DNA direct repeat elements with different spacings. Nat Struct Mol Biol 18:564-570
49. Rould MA, Perona JJ, Söll D, Steitz TA (1989) Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 A resolution. Science 246:1135-1142
50. Ruff M, Krishnaswamy S, Boeglin M, Poterszman A, Mitschler A, Podjarny A, Rees B, Thierry JC, Moras D (1991) Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Science 252:1682-1689
51. Santos GM, Fairall L, Schwabe JW (2011) Negative regulation by nuclear receptors: a plethora of mechanisms. Trends Endocrinol Metab 22:87-93
52. Sato Y, Ramalanjaona N, Huet T, Potier N, Osz J, Antony P, Peluso-Iltis C, Poussin- Courmontagne P, Ennifar E, Mély Y, Dejaegere A, Moras D, Rochel N (2010) The phantom effect of the Rexinoid LG100754: structural and functional insights. PLoS ONE 5:e15119
53. Schulman IG, Li C, Schwabe JW, Evans RM (1997) The phantom ligand effect: allosteric control of transcription by the retinoid X receptor. Genes Dev 11:299-308
54. Schwabe JW, Neuhaus D, Rhodes D (1990) Solution structure of the DNA-binding domain of the oestrogen receptor. Nature 348(6300):458-461
55. Svergun DI, Petoukhov MV, Koch MH, König S (2000) Crystal versus solution structures of thiamine diphosphate-dependent enzymes. J Biol Chem 275:297-302
56. Svergun DI, Petoukhov MV, Koch MH (2001) Determination of domain structure of proteins from X-ray solution scattering. Biophys J 80:2946-2953
57. Watson LC, Kuchenbecker KM, Schiller BJ, Gross JD, Pufall MA, Yamamoto KR (2013) The glucocorticoid receptor dimer interface allosterically transmits sequence-specific DNA signals. Nat Struct Mol Biol 20(7):876-883
58. Wurtz JM, Bourguet W, Renaud JP, Vivat V, Chambon P, Moras D, Gronemeyer H (1996) A canonical structure for the ligand-binding domain of nuclear receptors. Nat Struct Biol 3:87-94
59. Xu HE, Lambert MH, Montana VG, Plunket KD, Moore LB, Collins JL, Oplinger JA, Kliewer SA, Gampe RT Jr, McKee DD, Moore JT, Willson TM (2001) Structural determinants of ligand binding selectivity between the peroxisome proliferator-activated receptors. Proc Natl Acad Sci U S A 98:13919-13924
60. Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH, Noller HF (2001) Crystal structure of the ribosome at 5.5 A resolution. Science 292:883-896
61. Zhang J, Chalmers MJ, Stayrook KR, Burris LL, Wang Y, Busby SA, Pascal BD, Garcia- Ordo nez RD, Bruning JB, Istrate MA, Kojetin DJ, Dodge JA, Burris TP, Griffin PR (2011) DNA binding alters coactivator interaction surfaces of the intact VDR-RXR complex. Nat Struct Mol Biol 18:556-563