Uracil-DNA glycosylase-DNA substrate and product structures: Conformational strain promotes catalytic efficiency by coupled stereoelectronic effects

Proceedings of the National Academy of Sciences of the United States of America

Volumn 97, Issue 10, 2000, Pages 5083-5088

  Parikh, Sudip S ^a   Walcher, Gunter ^b   Jones, Garry D ^c   Slupphaug, Geir ^d   Krokan, Hans E ^d   Blackburn, G Michael ^b   Tainer, John A ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF SHEFFIELD   (United Kingdom)

^c Kodak Limited   (United Kingdom)

^d NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; URACIL DNA GLYCOSYLTRANSFERASE;

ARTICLE; CATALYSIS; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DEAMINATION; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME SUBSTRATE; EXCISION REPAIR; HUMAN; MACROMOLECULE; PRIORITY JOURNAL; PROTEIN DNA BINDING; SITE DIRECTED MUTAGENESIS; STEREOCHEMISTRY;

AMINO ACID SEQUENCE; BINDING SITES; CATALYSIS; CRYSTALLOGRAPHY, X-RAY; DNA; DNA GLYCOSYLASES; DNA REPAIR; HUMANS; MITOCHONDRIA; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; N-GLYCOSYL HYDROLASES; NUCLEIC ACID CONFORMATION; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; RECOMBINANT PROTEINS; URACIL-DNA GLYCOSIDASE;

EID: 0034625082     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.97.10.5083     Document Type: Article

References (45)

1. Davies, G. J., Mackenzie, L., Varrot, A., Dauter, M., Brzozowski, A. M., Schulein, M. & Withers, S. G. (1998) Biochemistry 37, 11707-11713.
2. Sidhu, G., Withers, S. G., Nguyen, N. T., McIntosh, L. P., Ziser, L. & Brayer, G. D. (1999) Biochemistry 38, 5346-5354.
3. Uitdehaag, J. C., Mosi, R., Kalk, K. H., vanderVeen, B. A., Dijkhuizen, L., Withers, S. G. & Dijkstra, B. W. (1999) Nat. Struct. Biol. 6, 432-436.
4. Fersht, A. (1999) Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding (Freeman, New York).
5. Kirby, A. J. (1983) The Anomeric Effect and Related Stereoelectronic Effects at Oxygen (Springer, Berlin).
6. Dunathan, H. C. (1966) Proc. Natl. Acad. Sci. USA 55, 712-716.
7. Weyand, M. & Schlichting, I. (1999) Biochemistry 38, 16469-16480.
8. Abe, I., Zheng, Y. F. & Prestwich, G. D. (1998) J. Enzym. Inhib. 13, 385-398.
9. Lee, A. Y., Stewart, J. D., Clardy, J. & Ganem, B. (1995) Chem. Biol. 2, 195-203.
10. Lindahl, T. & Wood, R. D. (1999) Science 286, 1897-1905.
11. Parikh, S. S., Mol, C. D. & Tainer, J. A. (1997) Structure (London) 5, 1543-1550.
12. Slupphaug, G., Eftedal, I., Kavli, B., Bharati, S., Helle, N. M., Haug, T., Levine, D. W. & Krokan, H. E. (1995) Biochemistry 34, 128-138.
13. Slupphaug, G., Mol, C. D., Kavli, B., Arvai, A. S., Krokan, H. E. & Tainer, J. A. (1996) Nature (London) 384, 87-92.
14. Parikh, S. S., Mol, C. D., Slupphaug, G., Bharati, S., Krokan, H. E. & Tainer, J. A. (1998) EMBO J. 17, 5214-5226.
15. Putnam, C. D., Shroyer, M. J., Lundquist, A. J., Mol, C. D., Arvai, A. S., Mosbaugh, D. W. & Tainer, J. A. (1999) J. Mol. Biol. 287, 331-346.
16. Parikh, S. S., Mol, C. D., Hosfield, D. J. & Tainer, J. A. (1999) Curr. Opin. Struct. Biol. 9, 37-47.
17. Mol, C. D., Izumi, T., Mitra, S. & Tainer, J. A. (2000) Nature (London) 403, 451-456.
18. Lindahl, T. (1990) Mutat. Res. 238, 305-311.
19. Xiao, W. & Samson, L. (1993) Proc. Natl. Acad. Sci. USA 90, 2117-2121.
20. Klinedinst, D. K. & Drinkwater, N. R. (1992) Mol. Carcinog. 6, 32-42.
21. Pourquier, P., Ueng, L-M., Kohlhagen, G., Mazumder, A., Gupta, M., Kohn, K. W. & Pommier, Y. (1997) J. Biol. Chem. 272, 7792-7796.
22. Kingma, P. S. & Osheroff, N. (1997) J. Biol. Chem. 272, 1148-1155.
23. Demple, B., Johnson, A. & Fung, D. (1986) Proc. Natl. Acad. Sci. USA 83, 7731-7735.
24. Loeb, L. A. (1985) Cell 40, 483-484.
25. Kingma, P. S., Corbett, A. H., Burcham, P. C., Marnett, L. J. & Osheroff, N. (1995) J. Biol. Chem. 270, 21441-21444.
26. Sawa, R., McAuley-Hecht, K., Brown, T. & Pearl, L. (1995) Nature (London) 373, 487-493.
27. Shroyer, M. J., Bennett, S. E., Putnam, C. D., Tainer, J. A. & Mosbaugh, D. W. (1999) Biochemistry 38, 4834-4845.
28. Drohat, A. C., Xiao, G., Tordova, M., Jagadeesh, J., Pankiewicz, K. W., Watanabe, K. A., Gilliland, G. L. & Stivers, J. T. (1999) Biochemistry 38, 11876-11886.
29. Luo, N., Mehler, E. & Osman, R. (1999) Biochemistry 38, 9209-9220.
30. Krokan, H. E., Standal, R. & Slupphaug, G. (1997) Biochem. J. 325, 1-16.
31. Zhang, H. C. & Daves, G. D. (1992) J. Org. Chem. 57, 4690-4696.
32. Otter, G. P., Elzagheid, M. I., Jones, G. D., MacCulloch, A. C., Walker, R. T., Oivanen, M. & Klika, K. D. (1998) J. Chem. Soc. Perkin Trans. 2, 2343-2349.
33. Nilsen, H., Yazdankhah, S. P., Eftedal, I. & Krokan, H. E. (1995) FEBS Lett. 362, 205-209.
34. Otwinowski, Z. & Minor, W. (1997) Methods Enzymol. 276, 307-326.
35. Navaza, J. (1994) Acta Crystallogr. A 50, 157-163.
36. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., et al. (1998) Acta Crystallogr. D 54, 905-921.
37. McRee, D. E. (1999) J. Struct. Biol. 125, 156-165.
38. Engh, R. A. & Huber, R. (1991) Acta Crystallogr. A 47, 392-400.
39. Stivers, J. T., Pankiewicz, K. W. & Watanabe, K. A. (1999) Biochemistry 38, 952-963.
40. Saenger, W. (1984) Principles of Nucleic Acid Structure (Springer, New York).
41. Andrews, C. W., Fraser-Reid, B. & Bowen, J. P. (1992) The Anomeric Effect and Associated Stereoelectronic Effects, in ACS Symposium Series No. 204, ed. Thatcher, G. R. J. (Am. Chem. Soc.), pp. 114-125.
42. Benner, S. A. (1988) in Mechanistic Principles of Enzyme Activity, eds. Liebman, J. F. & Greenberg, A. (VCH, New York), pp. 27-74.
43. Egert, E., Under, H. J., Hillen, W. & Bohm, M. C. (1980) J. Am. Chem. Soc. 102, 3707-3713.
44. Dawson, R. M. C., Elliott, D. C., Elliott, W. H. & Jones, K. M. (1959) Data for Biochemical Research (Clarendon, Oxford).
45. Schärer, O. D., Kawate, T., Gallinari, P., Jiricny, J. & Verdine, G. L. (1997) Proc. Natl. Acad. Sci. USA 94, 4878-4883.