Structural basis of natural promoter recognition by a unique nuclear receptor, HNF4α: Diabetes gene product

Journal of Biological Chemistry

Volumn 283, Issue 48, 2008, Pages 33685-33697

  Lu, Peng ^a   Rha, Geun Bae ^a   Melikishvili, Manana ^a   Wu, Guangteng ^a   Adkins, Brandon C ^a   Fried, Michael G ^a   Chi, Young In ^a  

^a UNIVERSITY OF KENTUCKY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CRYSTAL STRUCTURE; DNA;

DNA BINDING DOMAIN; DNA RESPONSE ELEMENT; HEPATOCYTE NUCLEAR FACTORS; MATURITY-ONSET DIABETES OF THE YOUNG; MOLECULAR FUNCTION; NUTRIENT TRANSPORT; PANCREATIC BETA CELLS; PROMOTER RECOGNITION;

GENES;

HEPATOCYTE NUCLEAR FACTOR 1ALPHA; HEPATOCYTE NUCLEAR FACTOR 4ALPHA;

ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; DIABETES MELLITUS; DNA BINDING; DNA RESPONSIVE ELEMENT; GENE MUTATION; HUMAN; HUMAN CELL; MATURITY ONSET DIABETES OF THE YOUNG; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN METHYLATION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; SEQUENCE ALIGNMENT;

VERTEBRATA;

EID: 57749119545     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M806213200     Document Type: Article

References (80)

1. Benoit, G., Cooney, A., Giguere, V., Ingraham, H., Lazar, M., Muscat, G., Perlmann, T., Renaud, J. P., Schwabe, J., Sladek, F., Tsai, M. J., and Laudet, V. (2006) Pharmacol. Rev. 58, 798-836
2. Parviz, F., Matullo, C., Garrison, W. D., Savatski, L., Adamson, J. W., Ning, G., Kaestner, K. H., Rossi, J. M., Zaret, K. S., and Duncan, S. A. (2003) Nat. Genet. 34, 292-296
3. Garrison, W. D., Battle, M. A., Yang, C., Kaestner, K. H., Sladek, F. M., and Duncan, S. A. (2006) Gastroenterology 130, 1207-1220
4. Gupta, R. K., and Kaestner, K. H. (2004) Trends Mol. Med. 10, 521-524
5. Duncan, S. A., Nagy, A., and Chan, W. (1997) Development 124, 279-287
6. Chen, W. S., Manova, K., Weinstein, D. C., Duncan, S. A., Plump, A. S., Prezioso, V. R., Bachvarova, R. F., and Darnell, J. E., Jr. (1994) Genes Dev. 8, 2466-2477
7. Hayhurst, G. P., Lee, Y. H., Lambert, G., Ward, J. M., and Gonzalez, F. J. (2001) Mol. Cell Biol. 21, 1393-1403
8. Inoue, Y., Yu, A. M., Inoue, J., and Gonzalez, F. J. (2004) J. Biol. Chem. 279, 2480-2489
9. Inoue, Y., Yu, A. M., Yim, S. H., Ma, X., Krausz, K. W., Inoue, J., Xiang, C. C., Brownstein, M. J., Eggertsen, G., Bjorkhem, I., and Gonzalez, F. J. (2006) J. Lipid Res. 47, 215-227
10. Watt, A. J., Garrison, W. D., and Duncan, S. A. (2003) Hepatology 37, 1249-1253
11. Gonzalez, F. J. (2008) Drug Metab. Pharmacokinet. 23, 2-7
12. Kamiyama, Y., Matsubara, T., Yoshinari, K., Nagata, K., Kamimura, H., and Yamazoe, Y. (2007) Drug Metab. Pharmacokinet. 22, 287-298
13. Gragnoli, C., Lindner, T., Cockburn, B. N., Kaisaki, P. J., Gragnoli, F., Marozzi, G., and Bell, G. I. (1997) Diabetes 46, 1648-1651
14. Lahuna, O., Rastegar, M., Maiter, D., Thissen, J. P., Lemaigre, F. P., and Rousseau, G. G. (2000) Mol. Endocrinol. 14, 285-294
15. Kamiya, A., Inoue, Y., and Gonzalez, F. J. (2003) Hepatology 37, 1375-1384
16. Yamagata, K., Furuta, H., Oda, N., Kaisaki, P. J., Menzel, S., Cox, N. J., Fajans, S. S., Signorini, S., Stoffel, M., and Bell, G. I. (1996) Nature 384, 458-460
17. Miura, A., Yamagata, K., Kakei, M., Hatakeyama, H., Takahashi, N., Fukui, K., Nammo, T., Yoneda, K., Inoue, Y., Sladek, F. M., Magnuson, M. A., Kasai, H., Miyagawa, J., Gonzalez, F. J., and Shimomura, I. (2006) J. Biol. Chem. 281, 5246-5257
18. Gupta, R. K., Vatamaniuk, M. Z., Lee, C. S., Flaschen, R. C., Fulmer, J. T., Matschinsky, F. M., Duncan, S. A., and Kaestner, K. H. (2005) J. Clin. Invest. 115, 1006-1015
19. Kulkarni, R. N., and Kahn, C. R. (2004) Science 303, 1311-1312
20. Odom, D. T., Zizlsperger, N., Gordon, D. B., Bell, G. W., Rinaldi, N. J., Murray, H. L., Volkert, T. L., Schreiber, J., Rolfe, P. A., Gifford, D. K., Fraenkel, E., Bell, G. I., and Young, R. A. (2004) Science 303, 1378-1381
21. Boj, S. F., Parrizas, M., Maestro, M. A., and Ferrer, J. (2001) Proc. Natl. Acad. Sci. U. S. A. 98, 14481-14486
22. Vaxillaire, M., and Froguel, P. (2008) Endocr. Rev. 29, 254-264
23. Pearson, E. R., Pruhova, S., Tack, C. J., Johansen, A., Castleden, H. A., Lumb, P. J., Wierzbicki, A. S., Clark, P. M., Lebl, J., Pedersen, O., Ellard, S., Hansen, T., and Hattersley, A. T. (2005) Diabetologia 48, 878-885
24. Bain, D. L., Heneghan, A. F., Connaghan-Jones, K. D., and Miura, M. T. (2007) Annu. Rev. Physiol. 69, 201-220
25. Dhe-Paganon, S., Duda, K., Iwamoto, M., Chi, Y. I., and Shoelson, S. E. (2002) J. Biol. Chem. 277, 37973-37976
26. Duda, K., Chi, Y.-I., and Shoelson, S. E. (2004) J. Biol. Chem. 279, 23311-23316
27. Hertz, R., Magenheim, J., Berman, I., and Bar-Tana, J. (1998) Nature 392, 512-516
28. Petrescu, A. D., Hertz, R., Bar-Tana, J., Schroeder, F., and Kier, A. B. (2005) J. Biol. Chem. 280, 16714-16727
29. Petrescu, A. D., Hertz, R., Bar-Tana, J., Schroeder, F., and Kier, A. B. (2002) J. Biol. Chem. 277, 23988-23999
30. Schroeder, F., Huang, H., Hostetler, H. A., Petrescu, A. D., Hertz, R., Bar-Tana, J., and Kier, A. B. (2005) Lipids 40, 559-568
31. Hertz, R., Kalderon, B., Byk, T., Berman, I., Za'tara, G., Mayer, R., and Bar-Tana, J. (2005) J. Biol. Chem. 280, 24451-24461
32. Khorasanizadeh, S., and Rastinejad, F. (2001) Trends Biochem. Sci. 26, 384-390
33. Jiang, G., and Sladek, F. M. (1997) J. Biol. Chem. 272, 1218-1225
34. Holmbeck, S. M., Dyson, H. J., and Wright, P. E. (1998) J. Mol. Biol. 284, 533-539
35. Kritis, A. A., Argyrokastritis, A., Moschonas, N. K., Power, S., Katrakili, N., Zannis, V. I., Cereghini, S., and Talianidis, I. (1996) Gene (Amst.) 173, 275-280
36. Lu, P., Liu, J., Melikishvili, M., Fried, M. G., and Chi, Y. I. (2008) Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64, 313-317
37. Otwinowski, Z., and Minor, W. (1997) Methods Enzymol. 276, 307-326
38. Vagin, A., and Teplyakov, A. (1997) J. Appl. Crystallogr. 30, 1002-1025
39. Rastinejad, F., Wagner, T., Zhao, Q., and Khorasanizadeh, S. (2000) EMBO J. 19, 1045-1054
40. Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Acta Crystallogr. Sect. D Biol. Crystallogr. 54, 905-921
41. Jones, T. A., Zou, J. Y., Cowan, S. W., and Kjeldgaard. (1991) Acta Crystallogr. Sect. A 47, 110-119
42. Maxam, A. M., and Gilbert, W. (1977) Proc. Natl. Acad. Sci. U. S. A. 74, 560-564
43. Hellman, L. M., and Fried, M. G. (2007) Nat. Protoc. 2, 1849-1861
44. McGhee, J. D., and von Hippel, P. H. (1974) J. Mol. Biol. 86, 469-489
45. Tsodikov, O. V., Holbrook, J. A., Shkel, I. A., and Record, M. T., Jr. (2001) Biophys. J. 81, 1960-1969
46. Johnson, W. C. (1999) Proteins 35, 307-312
47. Sreerama, N., and Woody, R. W. (2000) Anal. Biochem. 287, 252-260
48. Mao, D., Wachter, E., and Wallace, B. A. (1982) Biochemistry 21, 4960-4968
49. Borges, J. C., Pereira, J. H., Vasconcelos, I. B., dos Santos, G. C., Olivieri, J. R., Ramos, C. H., Palma, M. S., Basso, L. A., Santos, D. S., and de Azevedo, W. F., Jr. (2006) Arch. Biochem. Biophys. 452, 156-164
50. Rastinejad, F., Perlmann, T., Evans, R. M., and Sigler, P. B. (1995) Nature 375, 203-211
51. Shaffer, P. L., and Gewirth, D. T. (2002) EMBO J. 21, 2242-2252
52. Lavery, R., and Sklenar, H. (1989) J. Biomol. Struct. Dyn. 6, 655-667
53. Shaffer, P. L., Jivan, A., Dollins, D. E., Claessens, F., and Gewirth, D. T. (2004) Proc. Natl. Acad. Sci. U. S. A. 101, 4758-4763
54. Devarakonda, S., Harp, J. M., Kim, Y., Ozyhar, A., and Rastinejad, F. (2003) EMBO J. 22, 5827-5840
55. Roemer, S. C., Donham, D. C., Sherman, L., Pon, V. H., Edwards, D. P., and Churchill, M. E. (2006) Mol. Endocrinol. 20, 3042-3052
56. Glass, C. K., Rose, D. W., and Rosenfeld, M. G. (1997) Curr. Opin. Cell Biol. 9, 222-232
57. Zamir, I., Zhang, J., and Lazar, M. A. (1997) Genes Dev. 11, 835-846
58. Bogan, A. A., Dallas-Yang, Q., Ruse, M. D., Jr., Maeda, Y., Jiang, G., Nepomuceno, L., Scanlan, T. S., Cohen, F. E., and Sladek, F. M. (2000) J. Mol. Biol. 302, 831-851
59. Aggelidou, E., Iordanidou, P., Demetriades, C., Piltsi, O., and Hadzopoulou-Cladaras, M. (2006) FEBS J. 273, 1948-1958
60. Oxombre, B., Moerman, E., Eeckhoute, J., Formstecher, P., and Laine, B. (2002) J. Mol. Med. 80, 423-430
61. Zhao, Q., Chasse, S. A., Devarakonda, S., Sierk, M. L., Ahvazi, B., and Rastinejad, F. (2000) J. Mol. Biol. 296, 509-520
62. Miura, N., and Tanaka, K. (1993) Nucleic Acids Res. 21, 3731-3736
63. Tian, J. M., and Schibler, U. (1991) Genes Dev. 5, 2225-2234
64. Jakob, M., Kolodziejczyk, R., Orlowski, M., Krzywda, S., Kowalska, A., Dutko-Gwozdz, J., Gwozdz, T., Kochman, M., Jaskolski, M., and Ozyhar, A. (2007) Nucleic Acids Res. 35, 2705-2718
65. Zhao, Q., Khorasanizadeh, S., Miyoshi, Y., Lazar, M. A., and Rastinejad, F. (1998) Mol. Cell 1, 849-861
66. Chi, Y. I., Frantz, J. D., Oh, B. C., Hansen, L., Dhe-Paganon, S., and Shoelson, S. E. (2002) Mol. Cell 10, 1129-1137
67. Lu, P., Rha, G. B., and Chi, Y. I. (2007) Biochemistry 46, 12071-12080
68. Sladek, F. M., Dallas-Yang, Q., and Nepomuceno, L. (1998) Diabetes 47, 985-990
69. Vaxillaire, M., and Froguel, P. (2006) Endocrinol. Metab. Clin. North Am. 35, 371-384
70. Malecki, M. T., Yang, Y., Antonellis, A., Curtis, S., Warram, J. H., and Krolewski, A. S. (1999) Diabet. Med. 16, 193-200
71. Oxombre, B., Kouach, M., Moerman, E., Formstecher, P., and Laine, B. (2004) Biochem. J. 383, 573-580
72. Monney, C. T., Kaltenrieder, V., Cousin, P., Bonny, C., and Schorderet, D. F. (2002) Hum. Mutat. 20, 230-231
73. Pruhova, S., Ek, J., Lebl, J., Sumnik, Z., Saudek, F., Andel, M., Pedersen, O., and Hansen, T. (2003) Diabetologia 46, 291-295
74. Rochette-Egly, C. (2005) J. Biol. Chem. 280, 32565-32568
75. Torchia, J., Glass, C., and Rosenfeld, M. G. (1998) Curr. Opin. Cell Biol. 10, 373-383
76. Guo, H., Gao, C., Mi, Z., Wai, P. Y., and Kuo, P. C. (2006) Biochem. J. 394, 379-387
77. Hong, Y. H., Varanasi, U. S., Yang, W., and Leff, T. (2003) J. Biol. Chem. 278, 27495-27501
78. Viollet, B., Kahn, A., and Raymondjean, M. (1997) Mol. Cell Biol. 17, 4208-4219
79. Sun, K., Montana, V., Chellappa, K., Brelivet, Y., Moras, D., Maeda, Y., Parpura, V., Paschal, B. M., and Sladek, F. M. (2007) Mol. Endocrinol. 21, 1297-1311
80. Barrero, M. J., and Malik, S. (2006) Mol. Cell 24, 233-243