Direct evidence for methyl group coordination by carbon-oxygen hydrogen bonds in the lysine methyltransferase SET7/9

Journal of Biological Chemistry

Volumn 286, Issue 21, 2011, Pages 18658-18663

  Horowitz, Scott ^b   Yesselman, Joseph D ^b   Al Hashimi, Hashim M ^b   Trievel, Raymond C ^a  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALKYLATION; AMINO ACIDS; CATALYSTS; CRYSTAL ATOMIC STRUCTURE; ENZYMES; FUNCTIONAL GROUPS; HYDROGEN; OXYGEN; PROTEINS; QUANTUM THEORY; THERMOANALYSIS;

ACTIVE SITE; COFACTOR BINDING; HYDROGEN ATOMS; HYDROGEN BONDINGS; HYDROGEN-BOND FORMATION; METHYL GROUP; METHYL HYDROGEN ATOMS; METHYLTRANSFERASES; QUANTUM MECHANICS; S-ADENOSYLMETHIONINE; SITE-SPECIFIC; THERMO DYNAMIC ANALYSIS; X RAY CRYSTAL STRUCTURES;

HYDROGEN BONDS;

HISTONE LYSINE METHYLTRANSFERASE; S ADENOSYLMETHIONINE; S ADENOSYLMETHIONINE LYSINE METHYLTRANSFERASE 7; S ADENOSYLMETHIONINE LYSINE METHYLTRANSFERASE 9; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; HYDROGEN BOND; LIGAND BINDING; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTON NUCLEAR MAGNETIC RESONANCE; QUANTITATIVE STUDY; QUANTUM MECHANICS; STRUCTURE ANALYSIS; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

EID: 84961978260     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M111.232876     Document Type: Article

References (72)

1. Albert, M., and Helin, K. (2010) Semin. Cell Dev. Biol. 21, 209-220
2. Dillon, S. C., Zhang, X., Trievel, R. C., and Cheng, X. D. (2005) Genome Biol. 6, 227
3. Pradhan, S., Chin, H. G., Esteve, P. O., and Jacobsen, S. E. (2009) Epigenetics 4, 282-285
4. Kwon, T., Chang, J. H., Kwak, E., Lee, C. W., Joachimiak, A., Kim, Y. C., Lee, J., and Cho, Y. (2003) EMBO J. 22, 292-303
5. Xiao, B., Jing, C., Wilson, J. R., Walker, P. A., Vasisht, N., Kelly, G., Howell, S., Taylor, I. A., Blackburn, G. M., and Gamblin, S. J. (2003) Nature 421, 652-656
6. Couture, J. F., Hauk, G., Thompson, M. J., Blackburn, G. M., and Trievel, R. C. (2006) J. Biol. Chem. 281, 19280-19287
7. Subramanian, K., Jia, D., Kapoor-Vazirani, P., Powell, D. R., Collins, R. E., Sharma, D., Peng, J., Cheng, X., and Vertino, P. M. (2008) Mol. Cell 30, 336-347
8. Jacobs, S. A., Harp, J. M., Devarakonda, S., Kim, Y., Rastinejad, F., and Khorasanizadeh, S. (2002) Nat. Struct. Biol. 9, 833-838
9. Xiao, B., Jing, C., Kelly, G., Walker, P. A., Muskett, F. W., Frenkiel, T. A., Martin, S. R., Sarma, K., Reinberg, D., Gamblin, S. J., and Wilson, J. R. (2005) Gene Dev. 19, 1444-1454
10. Hu, P., and Zhang, Y. K. (2006) J. Am. Chem. Soc. 128, 1272-1278
11. Guo, H. B., and Guo, H. (2007) Proc. Natl. Acad. Sci. U.S.A. 104, 8797-8802
12. Zhang, X., and Bruice, T. C. (2007) Biochemistry 46, 14838-14844
13. Hu, P., Wang, S., and Zhang, Y. (2008) J. Am. Chem. Soc. 130, 3806-3813
14. Ramachandran, G. N., and Sasisekharan, V. (1965) Biochim. Biophys. Acta 109, 314-316
15. Krimm, S. (1967) Science 158, 530-531
16. Desiraju, G. R. (1991) Acc. Chem. Res. 24, 290-296
17. Derewenda, Z., Lee, L., Kobos, P., and Derewenda, U. (1995) FASEB J. 9, A1246-1246
18. Jiang, L., and Lai, L. H. (2002) J. Biol. Chem. 277, 37732-37740
19. Derewenda, Z. S., Derewenda, U., and Kobos, P. M. (1994) J. Mol. Biol. 241, 83-93
20. Bond, C. S., Zhang, Y., Berriman, M., Cunningham, M. L., Fairlamb, A. H., and Hunter, W. N. (1999) Structure 7, 81-89
21. Bach, R. D., Thorpe, C., and Dmitrenko, O. (2002) J. Phys. Chem. B 106, 4325-4335
22. Meyer, P., Schneider, B., Sarfati, S., Deville-Bonne, D., Guerreiro, C., Boretto, J., Janin, J., Véron, M., and Canard, B. (2000) EMBO J. 19, 3520-3529
23. Ash, E. L., Sudmeier, J. L., Day, R. M., Vincent, M., Torchilin, E. V., Haddad, K. C., Bradshaw, E. M., Sanford, D. G., and Bachovchin, W. W. (2000) Proc. Natl. Acad. Sci. U.S.A. 97, 10371-10376
24. Quinn, J. R., Zimmerman, S. C., Del Bene, J. E., and Shavitt, I. (2007) J. Am. Chem. Soc. 129, 934-941
25. Benevides, J. M., and Thomas, G. J., Jr. (1988) Biochemistry 27, 3868-3873
26. Ghosh, A., and Bansal, M. (1999) J. Mol. Biol. 294, 1149-1158
27. Liu, H., Matsugami, A., Katahira, M., and Uesugi, S. (2002) J. Mol. Biol. 322, 955-970
28. Mizuno, K., Ochi, T., and Shindo, Y. (1998) J. Chem. Phys. 109, 9502-9507
29. Ratajczyk, T., Czerski, I., Kamienska-Trela, K., Szymanski, S., and Wojcik, J. (2005) Angew Chem. Int. Edit. 44, 1230-1232
30. Qingzhong, L., Wang, N., and Zhiwu, Y. (2007) J. Mol. Struct. 847, 68-74
31. Scheiner, S. (2005) J. Phys. Chem. B 109, 16132-16141
32. Desiraju, G. R. (1996) Acc. Chem. Res. 29, 441-449
33. Cordier, F., Barfield, M., and Grzesiek, S. (2003) J. Am. Chem. Soc. 125, 15750-15751
34. Sheppard, D., Li, D. W., Godoy-Ruiz, R., Brüschweiler, R., and Tugarinov, V. (2010) J. Am. Chem. Soc. 132, 7709-7719
35. Sukumar, N., Mathews, F. S., Langan, P., and Davidson, V. L. (2010) Proc. Natl. Acad. Sci. U.S.A. 107, 6817-6822
36. Scheiner, S. (2009) J. Phys. Chem. B 113, 10421-10427
37. Yates, J. R., Pham, T. N., Pickard, C. J., Mauri, F., Amado, A. M., Gil, A. M., and Brown, S. P. (2005) J. Am. Chem. Soc. 127, 10216-10220
38. Couture, J. F., Dirk, L. M., Brunzelle, J. S., Houtz, R. L., and Trievel, R. C. (2008) Proc. Natl. Acad. Sci. U.S.A. 105, 20659-20664
39. Del Rizzo, P. A., Couture, J. F., Dirk, L. M., Strunk, B. S., Roiko, M. S., Brunzelle, J. S., Houtz, R. L., and Trievel, R. C. (2010) J. Biol. Chem. 285, 31849-31858
40. Trievel, R. C., Beach, B. M., Dirk, L. M., Houtz, R. L., and Hurley, J. H. (2002) Cell 111, 91-103
41. Zhang, X., Yang, Z., Khan, S. I., Horton, J. R., Tamaru, H., Selker, E. U., and Cheng, X. D. (2003) Mol. Cell 12, 177-185
42. Trievel, R. C., Flynn, E. M., Houtz, R. L., and Hurley, J. H. (2003) Nat. Struct. Biol. 10, 545-552
43. Iwig, D. F., and Booker, S. J. (2004) Biochemistry 43, 13496-13509
44. Schalk-Hihi, C., and Markham, G. D. (1999) Biochemistry 38, 2542-2550
45. Chirlian, L. E., and Francl, M. M. (1987) J. Comput. Chem. 8, 894-905
46. Frisch, M. J., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Montgomery, J. A., Jr., Vreven, T., Kudin, K. N., Burant, J. C., Millam, J. M., Iyengar, S. S., Tomasi, J., Barone, V., Mennucci, B., Cossi, M., Scalmani, G., Rega, N., Petersson, G. A., Nakatsuji, H., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Klene, M., Li, X., Knox, J. E., Hratchian, H. P., Cross, J. B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R. E., Yazyev, O., Austin, A. J., Cammi, R., Pomelli, C., Ochterski, J. W., Ayala, P. Y., Morokuma, K., Voth, G. A., Salvador, P., Dannenberg, J. J., Zakrzewski, V. G., Dapprich, S., Daniels, A. D., Strain, M. C., Farkas, O., Malick, D. K., Rabuck, A. D., Raghavachari, K., Foresman, J. B., Ortiz, J. V., Cui, Q., Baboul, A. G., Clifford, S., Cioslowski, J., Stefanov, B. B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Martin, R. L., Fox, D. J., Keith, T., Al-Laham, M. A., Peng, C. Y., Nanayakkara, A., Challacombe, M., Gill, P. M., Johnson, B., Chen, W., Wong, M. W., Gonzalez, C., and Pople, J. A. (2004) Gaussian 03, Revision C. 02. Gaussian, Inc., Wallingford, CT
47. Brooks, B. R., Brooks, C. L., 3rd, Mackerell, A. D., Jr., Nilsson, L., Petrella, R. J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., Caflisch, A., Caves, L., Cui, Q., Dinner, A. R., Feig, M., Fischer, S., Gao, J., Hodoscek, M., Im, W., Kuczera, K., Lazaridis, T., Ma, J., Ovchinnikov, V., Paci, E., Pastor, R. W., Post, C. B., Pu, J. Z., Schaefer, M., Tidor, B., Venable, R. M., Woodcock, H. L., Wu, X., Yang, W., York, D. M., and Karplus, M. (2009) J. Comput. Chem. 30, 1545-1614
48. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L. (1983) J. Chem. Phys. 79, 926-935
49. Nosé, S., and Klein, M. L. (1986) Phys. Rev. B Condens. Matter 33, 339-342
50. Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., and Pedersen, L. G. (1995) J. Chem. Phys. 103, 8577-8593
51. Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., Shim, J., Darian, E., Guvench, O., Lopes, P., Vorobyov, I., and Mackerell, A. D., Jr. (2010) J. Comput. Chem. 31, 671-690
52. Markham, G. D., Norrby, P. O., and Bock, C. W. (2002) Biochemistry 41, 7636-7646
53. Becke, A. D. (1993) J. Chem. Phys. 98, 5648-5652
54. Ditchfield, R., Hehre, W. J., and Pople, J. A. (1971) J. Chem. Phys. 54, 724-728
55. Miertus, S., Scrocco, E., and Tomasi, J. (1981) Chem. Phys. 55, 117-129
56. Wolinski, K., Hinton, J. F., and Pulay, P. (1990) J. Am. Chem. Soc. 112, 8251-8260
57. Scheiner, S. (2010) Int. J. Quantum Chem. 110, 2775-2783
58. Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., and Ferrin, T. E. (2004) J. Comput. Chem. 25, 1605-1612
59. Binkley, J. S., Pople, J. A., and Hehre, W. J. (1980) J. Am. Chem. Soc. 102, 939-947
60. Clark, T., Chandrasekhar, J., Spitznagel, G. W., and Schleyer, P. V. (1983) J. Comput. Chem. 4, 294-301
61. Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A. (1995) J. Biomol. NMR 6, 277-293
62. Goddard, T. G., and Kneller D. G. (2006) SPARKY 3. University of California, San Francisco
63. Markham, G. D., Hafner, E. W., Tabor, C. W., and Tabor, H. (1980) J. Biol. Chem. 255, 9082-9092
64. Park, J., Tai, J. Z., Roessner, C. A., and Scott, A. I. (1995) Bioorg. Med. Chem. Lett. 5, 2203-2206
65. Seeger, K., Lein, S., Reuter, G., and Berger, S. (2005) Biochemistry 44, 6208-6213
66. Peralta, J. E., de Azua, M. C. R., and Contreras, R. H. (1999) J. Mol. Struc- Theochem. 491, 23-31
67. Harris, R. K. (1983) Nuclear Magnetic Resonance Spectroscopy, Pitman Books Ltd., London
68. Scheiner, S., Gu, Y., and Kar, T. (2000) J. Mol. Struct. 500, 441-452
69. Afonin, A. V., Ushakov, I. A., Kuznetsova, S. Y., Petrova, O. V., Schmidt, E. Y., and Mikhaleva, A. I. (2002) Magn. Reson. Chem. 40, 114-122
70. Sigalov, M., Vashchenko, A., and Khodorkovsky, V. (2005) J. Org. Chem. 70, 92-100
71. Afonin, A. V., Ushakov, I. A., Vashchenko, A. V., Simonenko, D. E., Ivanov, A. V., Vasil'tsov, A. M., Mikhaleva, A. I., and Trofimov, B. A. (2009) Magn. Reson. Chem. 47, 105-112
72. Sarkhel, S., and Desiraju, G. R. (2004) Proteins 54, 247-259