Structure of a DNA glycosylase searching for lesions

Science

Volumn 311, Issue 5764, 2006, Pages 1153-1157

  Banerjee, Anirban ^a   Santos, Webster L ^a   Verdine, Gregory L ^a,b  

^a HARVARD UNIVERSITY   (United States)

^b HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL CULTURE; CROSSLINKING; ENZYME KINETICS;

DISULFIDE CROSS-LINKING (DXL); DNA GLYCOSYLASES;

DNA;

BACTERIAL ENZYME; DISULFIDE; DNA; DNA GLYCOSYLTRANSFERASE; NUCLEIC ACID BASE; PROTEIN MUTM; UNCLASSIFIED DRUG;

MEDICINE;

ARTICLE; BASE PAIRING; DNA CROSS LINKING; DNA DAMAGE; DNA HELIX; ENZYME STRUCTURE; GEOBACILLUS STEAROTHERMOPHILUS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA INTERACTION;

BACILLUS STEAROTHERMOPHILUS; BASE PAIRING; BINDING SITES; CROSS-LINKING REAGENTS; CRYSTALLOGRAPHY, X-RAY; DNA; DNA DAMAGE; DNA GLYCOSYLASES; GUANINE; HYDROGEN BONDING; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; OLIGODEOXYRIBONUCLEOTIDES; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY;

BACTERIA (MICROORGANISMS); GEOBACILLUS STEAROTHERMOPHILUS;

EID: 33644511436     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.1120288     Document Type: Article

References (35)

1. G. L. Verdine, S. D. Bruner, Chem. Biol. 4, 329 (1997).
2. D. O. Zharkov, A. P. Grollman, Mutat. Res. 577, 24 (2005).
3. L. A. Lipscomb et al., Proc. Natl. Acad. Sci. U.S.A. 92, 719 (1995).
4. Y. Oda et al., Nucleic Adds Res. 19, 1407 (1991).
5. G. E. Plum, A. P. Grollman, F. Johnson, K. J. Breslauer, Biochemistry 34, 16148 (1995).
6. S. S. Parikh, C. D. Putnam, J. A. Tainer, Mutat. Res. 460, 183 (2000).
7. J. T. Stivers, Prog. Nucleic Acid Res. Mol. Biol. 77, 37 (2004).
8. A. Banerjee, W. Yang, M. Karplus, G. L. Verdine, Nature 434, 612 (2005).
9. C. Cao, Y. L. Jiang, J. T. Stivers, F. Song, Nat. Struct. Mol. Biol. 11, 1230 (2004).
10. J. C. Fromme, G. L. Verdine, J. Biol. Chem. 278, 51543 (2003).
11. S. D. Bruner, D. P. Norman, G. L. Verdine, Nature 403, 859 (2000).
12. J. C. Fromme, G. L. Verdine, Adv. Protein Chem. 69, 1 (2004).
13. J. L. Huffman, O. Sundheim, J. A. Tainer, Mutat. Res. 577, 55 (2005).
14. J. Tchou et al., J. Biol. Chem. 269, 15318 (1994).
15. M. Bhagwat, J. A. Gerlt, Biochemistry 35, 659 (1996).
16. S. Boiteux, T. R. O'Connor, F. Lederer, A. Gouyette, J. Laval, J. Biol. Chem. 265, 3916 (1990).
17. D. O. Zharkov, R. A. Rieger, C. R. Iden, A. P. Grollman, J. Biol. Chem. 272, 5335 (1997).
18. F. Coste et al., J. Biol. Chem. 279, 44074 (2004).
19. J. C. Fromme, G. L. Verdine, Nat. Struct. Biol. 9, 544 (2002).
20. R. Gilboa et al., J. Biol. Chem. 277, 19811 (2002).
21. L. Serre, K. Pereira de Jesus, S. Boiteux, C. Zelwer, B. Castaing, EMBO J. 2l, 2854 (2002).
22. The oligonucleotides were synthesized using an automated synthesis procedure based on established chemistry (23-25). The synthesis was carried out on an ABI 392 synthesizer by modifying a regular 1 μM scale synthesis protocol to perform an H-phosphonate coupling step, followed by oxidation using carbon tetrachloride and diamine disulfide (free base) at the site of tether incorporation. (See the supplementary material for additional details.)
23. F. R. Atherton, H. T. Openshaw, A. R. Todd, J. Chem. Soc. 1945, 660 (1945).
24. B. C. Froehler, M. D. Matteucci, Tetrahedron Lett. 27, 469 (1986).
25. R. L. Letsinger, M. E. Schott, J. Am. Chem. Soc. 103, 7394 (1981).
26. A. Banerjee, G. L. Verdine, unpublished data.
27. A. Banerjee, W. L. Santos, G. L. Verdine, data not shown.
28. O. S. Fedorova et al., Biochemistry 41, 1520 (2002).
29. A. A. Ishchenko et al., Biochemistry 41, 7540 (2002).
30. D. T. Gewirth, P. B. Sigler, Nat. Struct. Biol. 2, 386 (1995).
31. C. He et al., Mol. Cell 20, 117 (2005).
32. C. G. Kalodimos et al., Science 305, 386 (2004).
33. H. Viadiu, A. K. Aggarwal, Mol. Cell 5, 889 (2000).
34. F. K. Winkler et al., EMBO J. 12, 1781 (1993).
35. Supported by NIH grant GM044853. For help during data collection and processing, we thank M. Becker and all the staff members at National Synchrotron Light Source beamline X25; C. Heaton, B. Miller, and staff members at Chess A1 beamline; and C. Ogata and N. Sukumar at APS 8BM beamline. We also thank Y. Korkhin for help and advice; Enanta Pharmaceutical for use of their x-ray facilities for initial characterization of the crystals; and C. Fromme, P. Blainey, and M. Spong for discussions and suggestions on the manuscript Coordinates and structure factors have been deposited in the Protein Data Bank with accession codes 2FSS (CC1), 2F5Q (CC2), 2F5N (IC1), 2F5P (IC2), and 2F50 (IC3).