Critical role of magnesium ions in DNA polymerase β's closing and active site assembly

Journal of the American Chemical Society

Volumn 126, Issue 27, 2004, Pages 8441-8453

  Yang, Linjing ^a   Arora, Karunesh ^a   Beard, William A ^b   Wilson, Samuel H ^b   Schlick, Tamar ^a  

^a NEW YORK UNIVERSITY   (United States)

^b NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOSYNTHESIS; CONFORMATIONS; ENZYMES; FUNCTIONS; IONS; MAGNESIUM PRINTING PLATES;

CONFORMATIONAL TRANSITIONS; DYNAMICS SIMULATIONS;

DNA;

DNA; DNA DIRECTED DNA POLYMERASE BETA; DNA POLYMERASE; MAGNESIUM ION; NUCLEOTIDE;

ARTICLE; CATALYSIS; CHEMICAL REACTION; COMPLEX FORMATION; CRYSTAL; DNA PROTEIN COMPLEX; ENZYME ACTIVE SITE; GEOMETRY; MOLECULAR DYNAMICS; SYNTHESIS; X RAY CRYSTALLOGRAPHY;

BINDING SITES; CATALYSIS; DNA; DNA POLYMERASE BETA; DNA REPAIR; MAGNESIUM; MODELS, MOLECULAR; NUCLEOTIDES; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY;

EID: 3142702966     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja049412o     Document Type: Article

References (75)

1. Cowan, J. A. The Biological chemistry of magnesium; VCH publishers, Inc.: New York, 1995.
2. Cowan, J. A. Inorganic biochemistry. An introduction; VCH publishers, Inc.: New York, 1993.
3. Burgess, J. Ions in solution: basic principles of chemical interaction; Ellis Horwood, Ltd.: New York, 1988.
4. Delarue, M.; Poch, O.; Tordo, N.; Moras, D.; Argos, P. Protein Eng. 1990, 3, 461-467.
5. Ito, J.; Braithwaite, D. K. Nucleic Acids Res. 1991, 19, 4045-4057.
6. Braithwaite, D. K.; Ito, J. Nucleic Acids Res. 1993, 21, 787-802.
7. Joyce, C. M.; Steitz, T. A. Annu. Rev. Biochem. 1994, 63, 777-822.
8. Polesky, A. H.; Steitz, T. A.; Grindley, N. D.; Joyce, C. M. J. Biol. Chem. 1990, 265, 14579-14591.
9. Doublié, S.; Ellenberger, T. Curr. Opin. Struct. Biol. 1998, 8, 704-712.
10. Doublié, S.; Tabor, S.; Long, A. M.; Richardson, C. C.; Ellenberger, T. Nature 1998, 391, 251-258.
11. Li, Y.; Korolev, S.; Waksman, G. EMBO J. 1998, 17, 7514-7525.
12. Li, Y.; Mitaxov, V.; Waksman, G. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9491-9496.
13. Li, Y.; Waksman, G. Protein Sci. 2001, 10, 1225-1233.
14. Wang, J.; Satter, A. K. M. A.; Wang, C. C.; Karam, J. D.; Konigsberg, W. H.; Steitz, T. A. Cell 1997, 89, 1087-1099.
15. Sawaya, M. R.; Pelletier, H.; Kumar, A.; Wilson, S. H.; Kraut, J. Science 1994, 264, 1930-1935.
16. Sawaya, M. R.; Prasad, R.; Wilson, S. H.; Kraut, J.; Pelletier, H. Biochemistry 1997, 36, 11205-11215.
17. Pelletier, H.; Sawaya, M. R.; Kumar, A.; Wilson, S. H.; Kraut, J. Science 1994, 264, 1891-1903.
18. Ling, H.; Boudsocq, F.; Woodgate, R.; Yang, W. Cell 2001, 107, 91-102.
19. Huang, H.; Chopra, R.; Verdine, G. L.; Harrison, S. C. Science 1998, 282, 1669-1675.
20. Kuchta, R. D.; Benkovic, P.; Benkovic, S. J. Biochemistry 1988, 27, 6716-6725.
21. Dahlberg, M. E.; Benkovic, S. J. Biochemistry 1991, 30, 4835-4843.
22. Patel, S. S.; Wong, I. Johnson, K. A. Biochemistry 1991, 30, 511-525.
23. Kati, W. M.; Johnson, K. A.; Jerva, L. F.; Anderson, K. S. J. Biol. Chem. 1992, 267, 25988-25997.
24. Frey, M. W.; Sowers, L. C.; Millar, D. P.; Benkovic, S. J. Biochemistry 1995, 34, 9185-9192.
25. Wemeburg, B. G.; Ahn, J.; Zhong, X.; Hondal, R. J.; Kraynov, V. S.; Tsai, M.-D. Biochemistry 1996, 35, 7041-7050.
26. Zhong, X.; Patel, S.S.; Werneburg, B. G.; Tsai, M.-D. Biochemistry 1997, 36, 11891-11900.
27. Vande Berg, B. J.; Beard, W. A.; Wilson, S. H. J. Biol. Chem. 2001, 276, 3408-3416.
28. Koshland, D. E. Angew Chem., Int. Ed. Engl. 1994, 33, 2375-2378.
29. Wong, I.; Patel, S. S.; Johnson, K. A. Biochemistry 1991, 30, 526-537.
30. Echols, H.; Goodman, M. F. Annu. Rev. Biochem. 1991, 60, 477-511.
31. Beard, W. A.; Wilson, S. H. Chem. Biol. 1998, 5, R7-R13.
32. Steitz, T. A. Curr. Opin. Struct. Biol. 1993, 3, 31-38.
33. Beard, W. A.; Wilson, S. H. Structure 2003, 11, 489-496.
34. Florián, J.; Goodman, M. F.; Warshel, A. J. Am. Chem. Soc. 2003, 125, 8163-8177.
35. Garcia-Viloca, M.; Gao, J.; Karplus, M.; Truhlar, D. G. Science 2003, 303, 186-194.
36. Warshel, A. Computer Modeling of Chemical Reactions in Enzymes and Solutions. John Wiley & Sons: New York, 1991.
37. Florián, J.; Goodman, M. F.; Warshel, A. Biopolymers 2003, 68, 286-299.
38. Ahn, J.; Werneburg, B. G.; Tsai, M.-D. Biochemistry 1997, 36, 1100-1107.
39. Ahn, J.; Kraynov, V. S.; Zhong, X.; Wemeburg, B. G.; Tsai, M.-D. Biochem. J. 1998, 331, 79-87.
40. Shah, A. M.; Li, S.-X.; Anderson, K. S.; Sweasy, J. B. J. Biol. Chem. 2001, 276, 10824-10831.
41. Krahn, J. M.; Beard, W. A.; Miller, H.; Grollman, A. P.; Wilson, S. H. Structure 2003, 1, 121-127.
42. Beard, W. A.; Wilson, S. H. Mutat. Res. 2000, 460, 231-244.
43. Ollis, D. L.; Brick, P.; Hamlin, R.; Xuong, N. G.; Steitz, T. A. Nature 1985, 313. 762-766.
44. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
45. Store, R. H.; Karplus, M. Proteins 1995, 23, 12-31.
46. Mackerell, J. A. D. Phys. Chem. B 1997, 101, 646-650.
47. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res. 2000, 28, 235-242.
48. Yang, L.; Beard, W. A.; Wilson, S. H.; Broyde, S.; Schlick, T. J. Mol. Biol. 2002, 317, 651-671.
49. Yang, L.; Beard, W. A.; Wilson, S. H.; Roux, B.; Broyde, S.; Schlick, T. J. Mol. Biol. 2002, 321, 459-478.
50. Brünger, A. T.; Karplus, M. Proteins: Struct., Funct., Genet. 1988, 4, 148-156.
51. MacKerell, A. D., Jr.; Banavali, N. K. J. Comput. Chem. 2000, 21, 105-120.
52. Arora, K.; Schlick, T. The complete closing conformational transition pathway of polymerase β simulated using stochastic difference equation algorithm. In preparation.
53. Yang, L.; Beard, W. A.; Wilson, S. H.; Broyde, S.; Schlick, T. Biophys. J. 2004, 86, 1-17.
54. Schlick, T. In Reviews in Computational Chemistry; Lipkowitz, K. B.; Boyd, D. B., Eds.; VCH Publishers: New York, 1992; Vol. III, pp 1-71.
55. Schlick, T.; Barth, E.; Mandziuk, M. Annu. Rev. Biophys. Biomol. Struct. 1997, 26, 181-222.
56. Barth, E.; Schlick, T. J. Chem. Phys. 1998, 109, 1617-1632.
57. Barth, E.; Schlick, T. J. Chem. Phys. 1998, 109, 1633-1642.
58. Schlick, T. Structure 2001, 9, R45-R53.
59. Radhakrishnan, R.; Schlick, T. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 5970-5975.
60. Menge, K. L.; Hostomsky, Z.; Nodes, B. R.; Hudson, G. O.; Rahmati, S.; Moomaw, E. W.; Almassy, R. J.; Hostomska. Z. Biochemistry 1995, 34, 15934-15942.
61. Kool, E. T. Biopolymers 1998, 48, 3-17.
62. Kool, E. T.; Morales, J. C.; Guckian, K. M. Angew. Chem., Int. Ed. 2000, 39, 990-1009.
63. Kraynov, V. S.; Werneburg, B. G.; Zhong, X.; Lee, H.; Ahn, J.; Tsai, M.-D. Biochem. J. 1997, 323, 103-111.
64. Beard, W. A.; Osheroff, W. P.; Prasad, R.; Sawaya, M. R.; Jaju, M.; Wood, T. G.; Kraut, J.; Kunkel, T. A.; Wilson, S. H. J. Biol. Chem. 1996, 271, 12141-12144.
65. Beard, W. A.; Shock, D. D.; Yang, X.-P.; DeLauder, S. F.; Wilson, S. H. J. Biol. Chem. 2002, 277, 8235-8242.
66. Kraynov, V. S.; Showalter, A. K.; Liu, J.; Zhong, X.; Tsai, M.-D. Biochemisry 2000, 39, 16008-16015.
67. Osheroff, W. P.; Beard, W. A.; Yin, S.; Wilson, S. H.; Kunkel, T. A. J. Biol. Chem. 2000, 275, 28033-28038.
68. Osheroff, W. P.; Beard, W. A.; Wilson, S. H.; Kunket, T. A. J. Biol. Chem. 1999, 274, 20749-20752.
69. Kunkel, T. A.; Wilson, S. H. Nat. Struct. Biol. 1998, 5, 95-99.
70. Arndt, J. W.; Gong, W.; Zhong, X.; Showalter, A. K.; Liu, J.; Dunlap, C. A.; Lin, Z.; Paxson, C.; Tsai, M.-D.; Chan, M. K. Biochemistry 2001, 40, 5368-5375.
71. Johnson, K. A. Annu. Rev. Biochem. 1993, 62, 685-713.
72. Bryant, F. R.; Johnson, K. A.; Benkovic, S. J. Biochemistry 1983, 22, 3537-3546.
73. Showalter, A. K.; Tsai, M.-D. Biochemistry 2002, 41, 10571-10516.
74. Herschlag, D.; Piccirilli, J. A.; Cech, T. R. Biochemistry 1991, 30, 4844-4854.
75. Knowles, J. R. Annu. Rev. Biochem. 1980, 49, 877-919.