DNA polymerase β ribonucleotide discrimination insertion, misinsertion, extension, and coding

Journal of Biological Chemistry

Volumn 285, Issue 32, 2010, Pages 24457-24465

  Cavanaugh, Nisha A ^a   Beard, William A ^a   Wilson, Samuel H ^a  

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

Author keywords

[No Author keywords available]

Indexed keywords

CHEMOTHERAPEUTIC DRUGS; DNA POLYMERASE; DNA SYNTHESISS; ORDERS OF MAGNITUDE; PRIMER TERMINUS; RIBONUCLEOTIDES; SUGAR PUCKER; TEMPLATING; TRIPHOSPHATE; WATSON-CRICK BASE PAIRING;

DNA; GENES; NUCLEOTIDES; POLYMERS; SUGAR (SUCROSE);

FUNCTIONAL POLYMERS;

2',3' DIDEOXYNUCLEOSIDE DERIVATIVE; CYTARABINE TRIPHOSPHATE; DIDEOXYNUCLEOSIDE TRIPHOSPHATE; DIDEOXYNUCLEOTIDE; DNA DIRECTED DNA POLYMERASE BETA; RIBONUCLEOTIDE; SUGAR; UNCLASSIFIED DRUG; DNA; NUCLEIC ACID; PROTEIN BINDING;

AMINO TERMINAL SEQUENCE; ARTICLE; CONTROLLED STUDY; DNA CONFORMATION; DNA SYNTHESIS; EXTENSION GENE; GENE INSERTION; GENETIC CODE; HUMAN; PRIORITY JOURNAL; BIOLOGICAL MODEL; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; DNA DAMAGE; KINETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; PROTEIN CONFORMATION;

BASE SEQUENCE; DNA; DNA DAMAGE; DNA POLYMERASE BETA; HUMANS; KINETICS; MODELS, BIOLOGICAL; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; NUCLEIC ACIDS; PROTEIN BINDING; PROTEIN CONFORMATION; RIBONUCLEOTIDES;

EID: 77955297664     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M110.132407     Document Type: Article

References (63)

1. Ferraro, P., Franzolin, E., Pontarin, G., Reichard, P., and Bianchi, V. (2010) Nucleic Acids Res. 38, e85
2. Traut, T. W. (1994) Mol. Cell. Biochem. 140, 1-22
3. Astatke, M., Grindley, N. D., and Joyce, C. M. (1998) J. Mol. Biol. 278, 147-165
4. Astatke, M., Ng, K., Grindley, N. D., and Joyce, C. M. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 3402-3407
5. Gardner, A. F., Joyce, C. M., and Jack, W. E. (2004) J. Biol. Chem. 279, 11834-11842
6. Lim, S. E., and Copeland, W. C. (2001) J. Biol. Chem. 276, 23616-23623
7. Reid, R., Mar, E. C., Huang, E. S., and Topal, M. D. (1988) J. Biol. Chem. 263, 3898-3904
8. Yang, G., Franklin, M., Li, J., Lin, T. C., and Konigsberg, W. (2002) Biochemistry 41, 10256-10261
9. Beard, W. A., and Wilson, S. H. (2006) Chem. Rev. 106, 361-382
10. Beard, W. A., Shock, D. D., Yang, X. P., DeLauder, S. F., and Wilson, S. H. (2002) J. Biol. Chem. 277, 8235-8242
11. Batra, V. K., Beard, W. A., Shock, D. D., Pedersen, L. C., and Wilson, S. H. (2005) Structure 13, 1225-1233
12. Batra, V. K., Beard, W. A., Shock, D. D., Krahn, J. M., Pedersen, L. C., and Wilson, S. H. (2006) Structure 14, 757-766
13. Batra, V. K., Beard, W. A., Shock, D. D., Pedersen, L. C., and Wilson, S. H. (2008) Mol. Cell 30, 315-324
14. Beard, W. A., and Wilson, S. H. (1998) Chem. Biol. 5, R7-R13
15. Beard, W. A., Shock, D. D., and Wilson, S. H. (2004) J. Biol. Chem. 279, 31921-31929
16. Beard, W. A., Osheroff, W. P., Prasad, R., Sawaya, M. R., Jaju, M., Wood, T. G., Kraut, J., Kunkel, T. A., and Wilson, S. H. (1996) J. Biol. Chem. 271, 12141-12144
17. Vande Berg, B. J., Beard, W. A., and Wilson, S. H. (2001) J. Biol. Chem. 276, 3408-3416
18. Beard, W. A., Shock, D. D., Batra, V. K., Pedersen, L. C., and Wilson, S. H. (2009) J. Biol. Chem. 284, 31680-31689
19. Kool, E. T. (2002) Annu. Rev. Biochem. 71, 191-219
20. Liang, F., Jain, N., Hutchens, T., Shock, D. D., Beard, W. A., Wilson, S. H., Chiarelli, M. P., and Cho, B. P. (2008) J. Med. Chem. 51, 6460-6470
21. McKenna, C. E., Kashemirov, B. A., Upton, T. G., Batra, V. K., Goodman, M. F., Pedersen, L. C., Beard, W. A., and Wilson, S. H. (2007) J. Am. Chem. Soc. 129, 15412-15413
22. Sucato, C. A., Upton, T. G., Kashemirov, B. A., Batra, V. K., Martínek, V., Xiang, Y., Beard, W. A., Pedersen, L. C., Wilson, S. H., McKenna, C. E., Florián, J., Warshel, A., and Goodman, M. F. (2007) Biochemistry 46, 461-471
23. Sucato, C. A., Upton, T. G., Kashemirov, B. A., Osuna, J., Oertell, K., Beard, W. A., Wilson, S. H., Florián, J., Warshel, A., McKenna, C. E., and Goodman, M. F. (2008) Biochemistry 47, 870-879
24. Upton, T. G., Kashemirov, B. A., McKenna, C. E., Goodman, M. F., Prakash, G. K., Kultyshev, R., Batra, V. K., Shock, D. D., Pedersen, L. C., Beard, W. A., and Wilson, S. H. (2009) Org. Lett. 11, 1883-1886
25. Moon, A. F., Garcia-Diaz, M., Batra, V. K., Beard, W. A., Bebenek, K., Kunkel, T. A., Wilson, S. H., and Pedersen, L. C. (2007) DNA Repair 6, 1709-1725
26. Beard, W. A., and Wilson, S. H. (1995) Methods Enzymol. 262, 98-107
27. Nick McElhinny, S. A., and Ramsden, D. A. (2003) Mol. Cell. Biol. 23, 2309-2315
28. Lim, S. E., Ponamarev, M. V., Longley, M. J., and Copeland, W. C. (2003) J. Mol. Biol. 329, 45-57
29. Tabor, S., and Richardson, C. C. (1995) Proc. Natl. Acad. Sci. U.S.A. 92, 6339-6343
30. Beard, W. A., Shock, D. D., Vande Berg, B. J., and Wilson, S. H. (2002) J. Biol. Chem. 277, 47393-47398
31. Bonnin, A., Lázaro, J. M., Blanco, L., and Salas, M. (1999) J. Mol. Biol. 290, 241-251
32. Boyer, P. L., Sarafianos, S. G., Arnold, E., and Hughes, S. H. (2000) Proc. Natl. Acad. Sci. U.S.A. 97, 3056-3061
33. Cases-Gonzalez, C. E., Gutierrez-Rivas, M., and Ménendez-Arias, L. (2000) J. Biol. Chem. 275, 19759-19767
34. Brown, J. A., Fiala, K. A., Fowler, J. D., Sherrer, S. M., Newmister, S. A., Duym, W. W., and Suo, Z. (2010) J. Mol. Biol. 395, 282-290
35. Pelletier, H., Sawaya, M. R., Kumar, A., Wilson, S. H., and Kraut, J. (1994) Science 264, 1891-1903
36. Kuchta, R. D., Ilsley, D., Kravig, K. D., Schubert, S., and Harris, B. (1992) Biochemistry 31, 4720-4728
37. Roettger, M. P., Fiala, K. A., Sompalli, S., Dong, Y., and Suo, Z. (2004) Biochemistry 43, 13827-13838
38. Goodman, M. F., Keener, S., Guidotti, S., and Branscomb, E. W. (1983) J. Biol. Chem. 258, 3469-3475
39. Harrington, C., and Perrino, F. W. (1995) J. Biol. Chem. 270, 26664-26669
40. Doublié, S., Tabor, S., Long, A. M., Richardson, C. C., and Ellenberger, T. (1998) Nature 391, 251-258
41. Kiefer, J. R., Mao, C., Braman, J. C., and Beese, L. S. (1998) Nature 391, 304-307
42. Li, Y., Korolev, S., and Waksman, G. (1998) EMBO J. 17, 7514-7525
43. Biswas, G., Iitaka, Y., Bose, A., and Banerjee, A. (1988) Acta Crystallogr. C. 44, 1269-1272
44. Williams, A. A., Darwanto, A., Theruvathu, J. A., Burdzy, A., Neidigh, J. W., and Sowers, L. C. (2009) Biochemistry 48, 11994-12004
45. Osheroff, W. P., Beard, W. A., Wilson, S. H., and Kunkel, T. A. (1999) J. Biol. Chem. 274, 20749-20752
46. Osheroff, W. P., Beard, W. A., Yin, S., Wilson, S. H., and Kunkel, T. A. (2000) J. Biol. Chem. 275, 28033-28038
47. Bergoglio, V., Ferrari, E., Hübscher, U., Cazaux, C., and Hoffmann, J. S. (2003) J. Mol. Biol. 331, 1017-1023
48. Horton, N. C., and Finzel, B. C. (1996) J. Mol. Biol. 264, 521-533
49. Ruiz, J. F., Juárez, R., García-Díaz, M., Terrados, G., Picher, A. J., González-Barrera, S., Fernández de Henestrosa, A. R., and Blanco, L. (2003) Nucleic Acids Res. 31, 4441-4449
50. Joyce, C. M. (1997) Proc. Natl. Acad. Sci. U.S.A. 94, 1619-1622
51. Fersht, A. R., Knill-Jones, J. W., and Tsui, W. C. (1982) J. Mol. Biol. 156, 37-51
52. Goodman, M. F., Creighton, S., Bloom, L. B., and Petruska, J. (1993) Crit. Rev. Biochem. Mol. Biol. 28, 83-126
53. Nakamura, J., and Swenberg, J. A. (1999) Cancer Res. 59, 2522-2526
54. Nick McElhinny, S. A., Watts, B. E., Kumar, D., Watt, D. L., Lundström, E. B., Burgers, P. M., Johansson, E., Chabes, A., and Kunkel, T. A. (2010) Proc. Natl. Acad. Sci. U.S.A. 107, 4949-4954
55. Sekiguchi, J., and Shuman, S. (1997) Mol. Cell 1, 89-97
56. Rydberg, B., and Game, J. (2002) Proc. Natl. Acad. Sci. U.S.A. 99, 16654-16659
57. Liu, Y., Beard, W. A., Shock, D. D., Prasad, R., Hou, E. W., and Wilson, S. H. (2005) J. Biol. Chem. 280, 3665-3674
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. Urban, M., Joubert, N., Purse, B. W., Hocek, M., and Kuchta, R. D. (2010) Biochemistry 49, 727-735
60. DeLucia, A. M., Grindley, N. D., and Joyce, C. M. (2003) Nucleic Acids Res. 31, 4129-4137
61. Gao, G., Orlova, M., Georgiadis, M. M., Hendrickson, W. A., and Goff, S. P. (1997) Proc. Natl. Acad. Sci. U.S.A. 94, 407-411
62. Sharma, B., Crespan, E., Villani, G., and Maga, G. (2008) Proteins 71, 715-727
63. Kirk, B. W., and Kuchta, R. D. (1999) Biochemistry 38, 7727-7736