Catalytic mechanisms of restriction and homing endonucleases

Biochemistry

Volumn 41, Issue 47, 2002, Pages 13851-13860

  Galburt, Eric A ^a   Stoddard, Barry L ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYTIC MECHANISMS;

CATALYST ACTIVITY; ENZYMES; TRANSPORT PROPERTIES;

BIOCHEMISTRY;

ENDONUCLEASE; HOMING ENDONUCLEASE; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE; UNCLASSIFIED DRUG;

ARTICLE; COMPARATIVE STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME DEGRADATION; ENZYME STRUCTURE; INTRON; MOLECULAR MECHANICS; PHASE TRANSITION; PRIORITY JOURNAL; PROTEIN MOTIF; PROTEIN PHOSPHORYLATION; RESTRICTION MAPPING; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; BINDING SITES; CATALYSIS; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DNA RESTRICTION ENZYMES; METALS; MODELS, MOLECULAR; PROTEIN CONFORMATION;

EID: 0037180394     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi020467h     Document Type: Article

References (75)

1. Westheimer, F. H. (1987) Science 235, 1173-1178.
2. Fersht, A. (1999) Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding, W. H. Freeman and Co., New York.
3. Silverman, R. B. (2000) The Organic Chemistry of Enzyme-Catalyzed Reactions, Academic Press, San Diego.
4. Rupert, P. B., and Ferre-D'Amare, A. R. (2001) Nature 410, 780786.
5. Murray, J. B., and Scott, W. G. (2000) J. Mol. Biol. 296, 33-41.
6. McClarin, J. A., Frederick, C. A., Wang, B. C., Greene, P., Boyer, H. W., Grable, J., and Rosenberg, J. M. (1986) Science 234, 1526-1541.
7. Winkler, F. K., Banner, D. W., Oefner, C., Tsemoglou, D., Brown, R. S., Heathman, S. P., Bryan, R. K., Martin, P. D., Petratos, K., and Wilson, K. S. (1993) EMBO J. 12, 1781-1795.
8. Grazulis, S., Deibert, M., Rimseliene, R., Skirgaila, R., Sasnauskas, G., Lagunavicius, A., Repin, V., Urbanke, C., Huber, R., and Siksnys, V. (2002) Nucleic Acids Res. 30, 876-885.
9. Cheng, X., Balendiran, K., Schildkraut, I., and Anderson, J. E. (1994) EMBO J. 13, 3927-3935.
10. Newman, M., Strzelecka, T., Dorner, L. F., Schildkraut, I., and Aggarwal, A. K. (1994) Structure 2, 439-452.
11. Wah, D. A., Hirsch, J. A., Dorner, L. F., Schildkraut, I., and Aggarwal, A. K. (1997) Nature 388, 97-100.
12. Bozic, D., Grazulis, S., Siksnys, V., and Huber, R. (1996) J. Mol. Biol. 255, 176-186.
13. Newman, M., Lunnen, K., Wilson, G., Greci, J., Schildkraut, I., and Phillips, S. E. (1998) EMBO J. 17, 5466-5476.
14. Deibert, M., Grazulis, S., Janulaitis, A., Siksnys, V., and Huber, R. (1999) EMBO J. 18, 5805-5816.
15. Deibert, M., Grazulis, S., Sasnauskas, G., Siksnys, V., and Huber, R. (2000) Nat. Struct. Biol. 7, 792-799.
16. Lukacs, C. M., Kucera, R., Schildkraut, I., and Aggarwal, A. K. (2000) Nat. Struct. Biol. 7, 134-140.
17. Huai, Q., Colandene, J. D., Topal, M. D., and Ke, H. (2001) Nat. Struct. Biol. 8, 665-669.
18. van der Woerd, M. J., Pelletier, J. J., Xu, S., and Friedman, A. M. (2001) Structure 9, 133-144.
19. Pingoud, A., and Jeltsch, A. (2001) Nucleic Acids Res. 29, 3705-3727.
20. Wittmayer, P. K., and Raines, R. T. (1996) Biochemistry 35, 1076-1083.
21. Flick, K. E., Jurica, M. S., Monnat, R. J., Jr., and Stoddard, B. L. (1998) Nature 394, 96-101.
22. Viadiu, H., and Aggarwal, A. K. (1998) Nat. Struct. Biol. 5, 910-916.
23. Horton, J. R., and Cheng, X. (2000) J. Mol. Biol. 300, 1049-1056.
24. Horton, N. C., and Perona, J. J. (2000) Proc. Natl. Acad. Sci. U.S.A. 97, 5729-5734.
25. Horton, N. C., Newberry, K. J., and Perona, J. J. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 13489-13494.
26. Kostrewa, D., and Winkler, F. K. (1995) Biochemistry, 34, 683-696.
27. Martin, A. M., Sam, M. D., Reich, N. O., and Perona, J. J. (1999) Nat. Struct. Biol. 6, 269-277.
28. Perona, J. J., and Martin, A. M. (1997) J. Mol. Biol. 273, 207-225.
29. Chevalier, B. S., Monnat, R. J., Jr., and Stoddard, B. L. (2001) Nat. Struct. Biol. 8, 312-316.
30. Jeltsch, A., Alves, J., Wolfes, H., Maass, G., and Pingoud, A. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 8499-8503.
31. Xu, S. Y., and Schildkraut, I. (1991) J. Biol. Chem. 266, 4425-4429.
32. Belfort, M., and Perlman, P. S. (1995) J. Biol. Chem. 270, 30237-30240.
33. Belfort, M., and Roberts, R. J. (1997) Nucleic Acids Res. 25, 3379-3388.
34. Chevalier, B. S., and Stoddard, B. L. (2001) Nucleic Acids Res. 29, 3757-3774.
35. Duan, X., Gimble, F. S., and Quiocho, F. A. (1997) Cell 89, 555-564.
36. Heath, P. J., Stephens, K. M., Monnat, R. J., Jr., and Stoddard, B. L. (1997) Nat. Struct. Biol. 4, 468-476.
37. Silva, G. H., Dalgaard, J. Z., Belfort, M., and Van Roey, P. (1999) J. Mol. Biol. 286, 1123-1136.
38. Ichiyanagi, K., Ishino, Y., Ariyoshi, M., Komori, K., and Morikawa, K. (2000) J. Mol. Biol. 300, 889-901.
39. Schweins, T., Langen, R., and Warshel, A. (1994) Nat. Struct. Biol. 1, 476-484.
40. Schweins, T., Geyer, M., Scheffzek, K., Warshel, A., Kalbitzer, H. R., and Wittinghofer, A. (1995) Nat. Struct. Biol. 2, 36-44.
41. Seligman, L. M., Stephens, K. M., Savage, J. H., and Monnat, R. J., Jr. (1997) Genetics 147, 1653-1664.
42. Turmel, M., Otis, C., Cote, V., and Lemieux, C. (1997) Nucleic Acids Res. 25, 2610-2619.
43. Elde, M., Haugen, P., Willassen, N. P., and Johansen, S. (1999) Eur. J. Biochem. 259, 281-288.
44. Elde, M., Willassen, N. P., and Johansen, S. (2000) Eur. J. Biochem. 267, 7257-7266.
45. Ellison, E. L., and Vogt, V. M. (1993) Mol. Cell. Biol. 13, 7531-7539.
46. Argast, G. M., Stephens, K. M., Emond, M. J., and Monnat, R. J., Jr. (1998) J. Mol. Biol. 280, 345-353.
47. Wittmayer, P. K., McKenzie, J. L., and Raines, R. T. (1998) Gene 206, 11-21.
48. Galburt, E. A., Chevalier, B., Tang, W., Jurica, M. S., Flick, K. E., Monnat, R. J., Jr., and Stoddard, B. L. (1999) Nat. Struct. Biol. 6, 1096-1099.
49. Mannino, S. J., Jenkins, C. L., and Raines, R. T. (1999) Biochemistry 38, 16178-16186.
50. Friedhoff, P., Franke, I., Krause, K. L., and Pingoud, A. (1999) FEBS Lett. 443, 209-214.
51. Friedhoff, P., Kolmes, B., Gimadutdinow, O., Wende, W., Krause, K. L., and Pingoud, A. (1996) Nucleic Acids Res. 24, 2632-2639.
52. Miller, M. D., Cai, J., and Krause, K. L. (1999) J. Mol. Biol. 288, 975-987.
53. Meiss, G., Gimadutdinow, O., Haberland, B., and Pingoud, A. (2000) J. Mol. Biol. 297, 521-534.
54. Eddy, S. R., and Gold, L. (1991) Genes Dev. 5, 1032-1041.
55. Goodrich-Blair, H., and Shub, D. A. (1996) Cell 84, 211-221.
56. Drouin, M., Lucas, P., Otis, C., Lemieux, C., and Turmel, M. (2000) Nucleic Acids Res. 28, 4566-4572.
57. Ko, T. P., Liao, C. C., Ku, W. Y., Chak, K. F., and Yuan, H. S. (1999) Structure 7, 91-102.
58. Kleanthous, C., Kuhlmann, U. C., Pommer, A. J., Ferguson, N., Radford, S. E., Moore, G. R., James, R., and Hemmings, A. M. (1999) Nat. Struct. Biol. 6, 243-252.
59. Kuhlmann, U. C., Moore, G. R., James, R., Kleanthous, C., and Hemmings, A. M. (1999) FEBS Lett. 463, 1-2.
60. Raaijmakers, H., Toro, I., Birkenbihl, R., Kemper, B., and Suck, D. (2001) J. Mol. Biol. 308, 311-323.
61. Hannan, J. P., Whittaker, S. B., Davy, S. L., Kuhlmann, U. C., Pommer, A. J., Hemmings, A. M., James, R., Kleanthous, C., and Moore, G. R. (1999) Protein Sci. 8, 1711-1713.
62. Garinot-Schneider, C., Pommer, A. J., Moore, G. R., Kleanthous, C., and James, R. (1996) J. Mol. Biol. 260, 731-742.
63. Pommer, A. J. (2001) J. Mol. Biol. 314, 735-749.
64. Derbyshire, V., Kowalski, J. C., Dansereau, J. T., Hauer, C. R., and Belfort, M. (1997) J. Mol. Biol. 265, 494-506.
65. Kowalski, J. C., Belfort, M., Stapleton, M. A., Holpert, M., Dansereau, J. T., Pietrokovski, S., Baxter, S. M., and Derbyshire, V. (1999) Nucleic Acids Res. 27, 2115-2125.
66. Van Roey, P., Waddling, C. A., Fox, K. M., Belfort, M., and Derbyshire, V. (2001) EMBO J. 20, 3631-3637.
67. Edgell, D. R., and Shub, D. A. (2001) Proc. Natl. Acad. Sci. U.S.A. 98, 7898-7903.
68. Dean, A. B., Stanger, M. J., Dansereau, J. T., Van Roey, P., Derbyshire, V., and Belfort, M. (2002) Proc. Natl. Acad. Sci. U.S.A. 99, 8554-8561.
69. Van Roey, P., Meehan, L., Kowalski, J. C., Belfort, M., and Derbyshire, V. (2002) Nat. Struct. Biol. 9 (11) (in press).
70. Glennon, T. M., Villa, J., and Warshel, A. (2000) Biochemistry 39, 9641-9651.
71. Dinner, A. R., Blackburn, G. M., and Karplus, M. (2001) Nature 413, 752-755.
72. Henkelman, G., Johannesson, G., and Jonsson, H. (2000) in Progress on Theoretical Chemistry and Physics (Schwartz, S. D., Ed.) pp 269, Kluwer Academic, Dordrecht, The Netherlands.
73. Kim, Y. C., Grable, J. C., Love, R., Greene, P. J., and Rosenberg, J. M. (1990) Science 249 (4974), 1307-1309.
74. Horton, N. C., Dorner, L. F., and Perona, J. J. (2002) Nat. Struct. Biol. 9 (1), 42-47.
75. Walker, D. C., Georgiou, T., Pommer, A. J., Walker, D., Moore, G. R., Kleanthous, C., and James, R. (2002) Nucleic Acids Res. 30 (14), 3225-3234.