Conformational changes during nucleotide selection by Sulfolobus solfataricus DNA polymerase Dpo4

Journal of Biological Chemistry

Volumn 284, Issue 31, 2009, Pages 21090-21099

  Eoff, Robert L ^a   Sanchez Ponce, Raymundo ^a,b   Guengerich, F Peter ^a  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b BRUKER DALTONIK GMBH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYTIC CYCLES; CONFORMATIONAL CHANGE; CONFORMATIONAL DYNAMICS; CONFORMATIONAL FLEXIBILITY; DEUTERIUM EXCHANGE; DNA POLYMERASE; FLUORESCENT PROBES; FUNCTION OF TIME; HYDROGEN-DEUTERIUM EXCHANGE; KINETIC DATA; KINETIC PROPERTIES; PHOSPHORYL TRANSFER; POLYMERASE FIDELITY; SOLVENT ACCESSIBILITY; STRUCTURAL CHANGE; SULFOLOBUS SOLFATARICUS; WATSON-CRICK BASE PAIRS;

DEUTERIUM; DNA; GENES; HYDROGEN; MASS SPECTROMETRY; NUCLEIC ACIDS; NUCLEOTIDES;

POLYMERS;

BACTERIAL DNA; DEOXYCYTIDINE PHOSPHATE; DNA POLYMERASE; DNA POLYMERASE 4; HELIX LOOP HELIX PROTEIN; MAGNESIUM ION; NUCLEOTIDE; PRIMER DNA; UNCLASSIFIED DRUG;

ARTICLE; BASE MISPAIRING; BASE PAIRING; CATALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; DEUTERIUM HYDROGEN EXCHANGE; DNA BINDING; DNA CONFORMATION; DNA STRUCTURE; DNA TEMPLATE; ENZYME SUBSTRATE; MASS SPECTROMETRY; MUTAGENESIS; NONHUMAN; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN TRANSPORT; SULFOLOBUS SOLFATARICUS;

AMINO ACID SEQUENCE; DEUTERIUM; DNA PRIMERS; DNA-DIRECTED DNA POLYMERASE; KINETICS; MAGNESIUM CHLORIDE; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; NUCLEOTIDES; PEPTIDES; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SULFOLOBUS SOLFATARICUS; TEMPLATES, GENETIC;

SULFOLOBUS SOLFATARICUS;

EID: 68949136996     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M109.009506     Document Type: Article

References (44)

1. Echols, H., and Goodman, M. F. (1991) Annu. Rev. Biochem. 60, 477-511
2. Kunkel, T. A. (2004) J. Biol. Chem. 279, 16895-16898
3. Joyce, C. M., and Benkovic, S. J. (2004) Biochemistry 43, 14317-14324
4. Tsai, Y. C., and Johnson, K. A. (2006) Biochemistry 45, 9675-9687
5. Beard, W. A., and Wilson, S. H. (2006) f Rev. 106, 361-382
6. Freisinger, E., Grollman, A. P., Miller, H., and Kisker, C. (2004) EMBO J. 23, 1494-1505
7. Friedberg, E. C., Fischhaber, P. L., and Kisker, C. (2001) Cell 107, 9-12
8. Yang, W., and Woodgate, R. (2007) Proc. Natl. Acad. Sci. U.S.A. 104, 15591-15598
9. Ohmori, H., Friedberg, E. C., Fuchs, R. P., Goodman, M. F., Hanaoka, F., Hinkle, D., Kunkel, T. A., Lawrence, C. W., Livneh, Z., Nohmi, T., Prakash, L., Prakash, S., Todo, T., Walker, G. C., Wang, Z., and Woodgate, R. (2001) Mol. Cell 8, 7-8
10. Lone, S., Townson, S. A., Uljon, S. N., Johnson, R. E., Brahma, A., Nair, D. T., Prakash, S., Prakash, L., and Aggarwal, A. K. (2007) Mol. Cell 25, 601-614
11. Nair, D. T., Johnson, R. E., Prakash, L., Prakash, S., and Aggarwal, A. K. (2005) Science 309, 2219-2222
12. Eoff, R. L., Irimia, A., Angel, K. C., Egli, M., and Guengerich, F. P. (2007) J. Biol. Chem. 282, 19831-19843
13. Eoff, R. L., Irimia, A., Egli, M., and Guengerich, F. P. (2007) J. Biol. Chem. 282, 1456-1467
14. Ling, H., Boudsocq, F., Woodgate, R., and Yang, W. (2001) Cell 107, 91-102
15. Ling, H., Boudsocq, F., Woodgate, R., and Yang, W. (2004) Mol. Cell 13, 751-762
16. Ling, H., Sayer, J. M., Plosky, B. S., Yagi, H., Boudsocq, F., Woodgate, R., Jerina, D. M., and Yang, W. (2004) Proc. Natl. Acad. Sci. U.S.A. 101, 2265-2269
17. Zang, H., Goodenough, A. K., Choi, J. Y., Irimia, A., Loukachevitch, L. V., Kozekov, I. D., Angel, K. C., Rizzo, C. J., Egli, M., and Guengerich, F. P. (2005) J. Biol. Chem. 280, 29750-29764
18. Zang, H., Irimia, A., Choi, J. Y., Angel, K. C., Loukachevitch, L. V., Egli, M., and Guengerich, F. P. (2006) J. Biol. Chem. 281, 2358-2372
19. Rechkoblit, O., Malinina, L., Cheng, Y., Kuryavyi, V., Broyde, S., Geacintov, N. E., and Patel, D. J. (2006) PLoS Biol. 4, e11
20. Wong, J. H., Fiala, K. A., Suo, Z., and Ling, H. (2008) J. Mol. Biol. 379, 317-330
21. Xing, G., Kirouac, K., Shin, Y. J., Bell, S. D., and Ling, H. (2009) Mol. Microbiol. 71, 678-691
22. Vaisman, A., Ling, H., Woodgate, R., and Yang, W. (2005) EMBO J. 24, 2957-2967
23. Fiala, K. A., and Suo, Z. (2004) Biochemistry 43, 2106-2115
24. Washington, M. T., Prakash, L., and Prakash, S. (2001) Cell 107, 917-927
25. Beckman, J. W., Wang, Q., and Guengerich, F. P. (2008) J. Biol. Chem. 283, 36711-36723
26. Busenlehner, L. S., and Armstrong, R. N. (2005) Arch. Biochem. Biophys. 433, 34-46
27. Busenlehner, L. S., Salomonsson, L., Brzezinski, P., and Armstrong, R. N. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 15398-15403
28. Hoofnagle, A. N., Resing, K. A., and Ahn, N. G. (2003) Annu. Rev. Biophys. Biomol. Struct. 32, 1-25
29. Lísal, J., Lam, T. T., Kainov, D. E., Emmett, M. R., Marshall, A. G., and Tuma, R. (2005) Nat. Struct. Mol. Biol. 12, 460-466
30. Sanchez-Ponce, R., and Guengerich, F. P. (2007) Anal. Chem. 79, 3355-3362
31. Englander, S. W. (2006) J. Am. Soc. Mass Spectrom. 17, 1481-1489
32. Johnson, K. A. (2008) J. Biol. Chem. 283, 26297-26301
33. Woodside, A. M., and Guengerich, F. P. (2002) Biochemistry 41, 1039-1050
34. Zhang, H., Eoff, R. L., Kozekov, I. D., Rizzo, C. J., Egli, M., and Guengerich, F. P. (2009) J. Biol. Chem. 284, 3563-3576
35. Alt, A., Lammens, K., Chiocchini, C., Lammens, A., Pieck, J. C., Kuch, D., Hopfner, K. P., and Carell, T. (2007) Science 318, 967-970
36. Avkin, S., and Livneh, Z. (2002) Mutat. Res. 510, 81-90
37. Choi, J. Y., Angel, K. C., and Guengerich, F. P. (2006) J. Biol. Chem. 281, 21062-21072
38. Ogi, T., Shinkai, Y., Tanaka, K., and Ohmori, H. (2002) Proc. Natl. Acad. Sci. U.S.A. 99, 15548-15553
39. Suzuki, N., Yasui, M., Santosh Laxmi, Y. R., Ohmori, H., Hanaoka, F., and Shibutani, S. (2004) Biochemistry 43, 11312-11320
40. Velasco-Miguel, S., Richardson, J. A., Gerlach, V. L., Lai, W. C., Gao, T., Russell, L. D., Hladik, C. L., White, C. L., and Friedberg, E. C. (2003) DNA Repair 2, 91-106
41. McAuley-Hecht, K. E., Leonard, G. A., Gibson, N. J., Thomson, J. B., Watson, W. P., Hunter, W. N., and Brown, T. (1994) Biochemistry 33, 10266-10270
42. Brieba, L. G., Eichman, B. F., Kokoska, R. J., Doublié, S., Kunkel, T. A., and Ellenberger, T. (2004) EMBO J. 23, 3452-3461
43. Furge, L. L., and Guengerich, F. P. (1997) Biochemistry 36, 6475-6487
44. DeLano, W. L. (2002) The PyMol Molecular Graphics System, DeLano Scientific, San Carlos, CA