Mechanisms of base selection by the Escherichia coli mispaired uracil glycosylase

Journal of Biological Chemistry

Volumn 283, Issue 14, 2008, Pages 8829-8836

  Liu, Pingfang ^a,c   Theruvathu, Jacob A ^a   Darwanto, Agus ^a   Lao, Victoria Valinluck ^a   Pascal, Tod ^b   Goddard III, William ^b   Sowers, Lawrence C ^a,b,d  

^a LOMA LINDA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^c HARVARD UNIVERSITY   (United States)

^d Alumni Hall for Basic Science ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI; HYDROCARBONS; HYDROGEN; MAINTENANCE; NUCLEIC ACIDS; OLIGONUCLEOTIDES; ORGANIC ACIDS; THERMODYNAMIC STABILITY;

BASE EXCISION REPAIRS; CLEAVAGE RATES; DNA GLYCOSYLASES; GLYCOSYLASE; HELIX FORMATIONS; HYDROGEN ATOMS; IN CELLS; LIVING ORGANISMS; METHYL GROUPS; METHYL SUBSTITUENTS; ORDERS OF MAGNITUDES; PARAMETERS IDENTIFIED; RELATIVE RATES; REPAIR SYSTEMS;

REPAIR;

ADENINE; DNA GLYCOSYLTRANSFERASE; GUANINE; HYDROGEN; METHYL GROUP; PURINE; THYMINE; URACIL; ESCHERICHIA COLI PROTEIN; MISMATCH SPECIFIC THYMINE URACIL DNA GLYCOSYLASE; MISMATCH-SPECIFIC THYMINE URACIL-DNA GLYCOSYLASE; NUCLEOTIDE; THYMINE DNA GLYCOSYLASE;

ARTICLE; BASE MISPAIRING; DNA REPAIR; ELECTRON TRANSPORT; ENZYME STABILITY; ESCHERICHIA COLI; MOLECULAR MECHANICS; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN CLEAVAGE; THERMODYNAMICS; BACTERIAL GENOME; CHEMISTRY; ENZYMOLOGY; KINETICS; METABOLISM; PHYSIOLOGY;

ESCHERICHIA COLI;

DNA REPAIR; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENOME, BACTERIAL; KINETICS; NUCLEOTIDES; THYMINE DNA GLYCOSYLASE;

EID: 44049101853     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M707174200     Document Type: Article

References (56)

1. Lindahl, T. (2000) Mutat. Res. 462, 129-135
2. Krokan, H. E., Nilsen, H., Skorpen, F., Otterlei, M., and Slupphaug, G. (2000) FEBS Lett. 476, 73-77
3. Sung, J. S., and Demple, B. (2006) FEBS J. 273, 1620-1629
4. Wilson, D. M., and Bohr, V. A. (2007) DNA Repair 6, 544-559
5. Saul, R. L., and Ames, B. N. (1986) Basic Life Sci. 38, 529-535
6. Mullaart, E., Lohman, P. H., Berends, F., and Vijg, J. (1990) Mutat. Res. 237, 189-210
7. Lindahl, T. (1980) Methods Enzymol. 65, 284-290
8. Caradonna, S. J., and Cheng, Y. C. (1980) J. Biol. Chem. 255, 2293-2300
9. Mosbaugh, D. W., and Bennett, S. E. (1994) Prog. Nucleic Acids Res. Mol. Biol. 48, 315-370
10. Pearl, L. H. (2000) Mutat. Res. 460, 165-181
11. Saava, R., McAuley-Hecht, K., Brown, T., and Pearl, L. (1995) Nature 373, 487-493
12. Nilsen, H., Otterlei, M., Haug, T., Solum, K., Nagelhus, T. A., Skorpen, F., and Krokan, H. E. (1997) Nucleic Acids Res. 25, 750-755
13. Sousa, M. M., Krokan, H. E., and Slupphaug, G. (2007) Mol. Aspects Med. 28, 276-306
14. Neddermann, P., and Jiricny, J. (1993) J. Biol. Chem. 268, 21218-21224
15. Bennett, M. T., Rodgers, M. T., Hebert, A. S., Ruslander, L. E., Eisele, L., and Drohat, A. C. (2006) J. Am. Chem. Soc. 128, 12510-12519
16. Nilsen, H., Haushalter, K. A., Robins, P., Barnes, D. E., Verdine, G. L., and Lindahl, T. (2001) EMBO J. 20, 4278-4286
17. Wibley, J. E., Walters, T. R., Haushalter, K., Verdine, G. L., and Pearl, L. H. (2003) Mol. Cell 11, 1647-1659
18. Boorstein, R. J., Cummings, A., Marenstein, D. R., Chan, M. K., Ma, Y., Neubert, T. A., Brown, S. M., and Teebor, G. W. (2001) J. Biol. Chem. 276, 41991-41997
19. Matsubara, M., Tanaka, T., Terato, H., Ohmae, E., Izumi, S., Katayanagi, K., and Ide, H. (2004) Nucleic Acids Res. 32, 5291-5302
20. Sung, J. S., and Mosbaugh, D. W. (2000) Biochemistry 39, 10224-10235
21. Hang, B., Downing, G., Guliaev, A. B., and Singer, B. (2002) Biochemistry 41, 2158-2165
22. O'Neill, R. J., Vorob'eva, O. V., Shahbakhti, H., Zmuda, E., Bhagwat, A. S., and Baldwin, G. S. (2003) J. Biol. Chem. 278, 20526-20532
23. Lari, S. U., Chen, C. Y., Vertessy, B. G., Morre, J., and Bennett, S. E. (2006) DNA Repair 5, 1407-1420
24. Barrett, T. E., Scharer, O. D., Savva, R., Brown, T., Jiricny, J., Verdine, G. L., and Pearl, L. H. (1999) EMBO J. 18, 6599-6609
25. Liu, P., Burdzy, A., and Sowers, L. C. (2002) Chem. Res. Toxicol. 15, 1001-1009
26. Gait, M. J. (ed) (1983) Oligonucleotide Synthesis: A Practical Approach, Oxford University Press, Oxford, NY
27. Fujimoto, J., Nuesca, Z., Mazurek, M., and Sowers, L. C. (1996) Nucleic Acids Res. 24, 754-759
28. Richard, E. G. (1975) in CRC Handbook of Biochemistry and Molecular Biology: Nucleic Acid (Fasman, G.D., ed) 3rd Ed., Vol. 1, p. 589, Cleveland, OH
29. Allawi, H. T., and SantaLucia, J. (1997) Biochemistry 36, 10581-10594
30. Watkins, N. E., Jr., and SantaLucia, J., Jr. (2005) Nucleic Acids Res. 33, 6258-6267
31. Eritja, R., Horowitz, D. M., Walker, P. A., Ziehler-Martin, P., Boosalis, M., Goodman, M. F., Itakura, K., and Kaplan, B. E. (1986) Nucleic Acids Res. 14, 8135-8153
32. Cheong, C., Tinoco, I., Jr., and Chollet, A. (1988) Nucleic Acids Res. 16, 5115-5122
33. Law, S. M., Eritja, R., Goodman, M. F., and Breslauer, K. J. (1996) Biochemistry 35, 12329-12337
34. Petruska, J., Sowers, L. C., and Goodman, M. F. (1986) Proc. Natl. Acad. Sci. U. S. A. 83, 1559-1562
35. Hansch, C., Leo, A., Unger, S. H., Kim, K. H., Nikaitani, D., and Lien, E. J. (1973) J. Med. Chem. 16, 1207-1216
36. Sober, H. A. (1970) Handbook of Biochemistry, pp. J3, The Chemical Rubber Co., Cleveland, OH
37. Valinluck, V., Wu, W., Liu, P., Neidigh, J. W., and Sowers, L. C. (2006) Chem. Res. Toxicol. 19, 556-562
38. Slupphaug, G., Mol, C. D., Kavli, B., Arvai, A. S., Krokan, H. E., and Tainer, J. A. (1996) Nature 384, 87-92
39. Wong, I., Lundquist, A. J., Bernards, A. S., and Mosbaugh, D. W. (2002) J. Biol. Chem. 277, 19424-19432
40. Sagi, J., Hang, B., and Singer, B. (1999) Chem. Res. Toxicol. 12, 917-923
41. Valinluck, V., Liu, P., Burdzy, A., Ryu, J., and Sowers, L. C. (2002) Chem. Res. Toxicol. 15, 1595-1601
42. Minetti, C. A., Remeta, D. P., Zharkov, D. O., Plum, G. E., Johnson, F., Grollman, A. P., and Breslauer, K. J. (2003) J. Mol. Biol. 328, 1047-1060
43. Krosky, D. J., Schwarz, F. P., and Stivers, J. T. (2004) Biochemistry 43, 4188-4195
44. Parker, J. B., Bianchet, M. A., Krosky, D. J., Freidman, J. I., Amzel, L. M., and Stivers, J. T. (2007) Nature 449, 433-438
45. Jang, Y. H., Sowers, L. C., Cagin, T., and Goddard, W. A., III (2001) J. Phys. Chem. 105, 274-280
46. Shapiro, R., and Kang, S. (1969) Biochemistry 8, 1806-1810
47. Sun, B., Latham, K. A., Dodson, M. L., and Lloyd, R. S. (1995) J. Biol. Chem. 270, 19501-19508
48. Dinner, A. R., Blackburn, G. M., and Karplus, M. (2001) Nature 413, 752-755
49. Bianchet, M. A., Seiple, L. A., Jiang, Y. L., Ichikawa, Y., Amzel, L. M., and Stivers, J. T. (2003) Biochemistry 42, 12455-12460
50. Liu, P., Burdzy, A., and Sowers, L. C. (2003) DNA Repair 2, 199-210
51. Parker, W. B., and Cheng, Y. C. (1990) Pharmacol. Ther. 48, 381-395
52. Seiple, L., Jaruga, P., Dizdaroglu, M., and Stivers, J. T. (2006) Nucleic Acids Res. 34, 140-151
53. Whiteman, M., Jenner, A., and Halliwell, B. (1997) Chem. Res. Toxicol. 10, 1240-1246
54. Jiang, Q., Blount, B. C., and Ames, B. N. (2003) J. Biol. Chem. 278, 32834-32840
55. Henderson, J. P., Byun, J., Williams, M. V., Mueller, D. M., McCormick, M. L., and Heinecke, J. W. (2001) J. Biol. Chem. 276, 7867-7875
56. Henderson, J. P., Byun, J., Takeshita, J., and Heinecke, J. W. (2003) J. Biol. Chem. 278, 23522-23528