Frameshift deletion by Sulfolobus solfataricus P2 DNA polymerase Dpo4 T239W is selective for purines and involves normal conformational change followed by slow phosphodiester bond formation

Journal of Biological Chemistry

Volumn 284, Issue 50, 2009, Pages 35144-35153

  Zhang, Huidong ^a,b   Beckman, Jeff W ^a,c   Guengerich, F Peter ^a  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Dept of Biological Chemistry and Molecular Pharmacology ^*  (United States)

^c YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE COMPLEXES; CONFORMATIONAL CHANGE; DNA ADDUCTS; DNA POLYMERASE; DRIVING FORCES; FRAMESHIFT; HIGHER FREQUENCIES; HUMAN DNA POLYMERASE; PHOSPHODIESTER BONDS; STEADY-STATE KINETICS; SULFOLOBUS SOLFATARICUS; TEMPLATING;

DNA; MASS SPECTROMETRY; NUCLEIC ACIDS; POLYMERS;

GENES;

DEOXYCYTIDINE KINASE; DNA POLYMERASE; DNA POLYMERASE DPO4; PHOSPHODIESTERASE; PURINE; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; CHEMICAL BOND; CONFORMATIONAL TRANSITION; DNA BINDING; FRAMESHIFT MUTATION; GENE DELETION; GENE FREQUENCY; GENE SEQUENCE; NONHUMAN; PRIORITY JOURNAL; STEADY STATE; SULFOLOBUS SOLFATARICUS;

ARCHAEAL PROTEINS; DNA POLYMERASE BETA; DNA, ARCHAEAL; FRAMESHIFT MUTATION; HUMANS; HYDROGEN BONDING; MOLECULAR STRUCTURE; NUCLEIC ACID CONFORMATION; PURINES; SULFOLOBUS SOLFATARICUS;

SULFOLOBUS SOLFATARICUS;

EID: 71749105337     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M109.067397     Document Type: Article

References (36)

1. Friedberg, E. C., Walker, G. C., Siede, W., Wood, R. D., Schultz, R. A., and Ellenberger, T. (eds) (2006) DNA Repair and Mutagenesis, 2nd Ed., American Society for Microbiology, Washington, D. C.
2. Loeb, L. A., and Christians, F. C. (1996) Mutat, Res. 350, 279-286
3. Bond, J. A., Gown, A. M., Yang, H. L., Benditt, E. P., and Juchau, M. R. (1981) J. Toxicol. Environ. Health 7, 327-335
4. Shigenaga, M. K., Hagen, T. M., and Ames, B. N. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 10771-10778
5. Woodgate, R. (1999) Genes Dev. 13, 2191-2195
6. Goodman, M. F. (2002) Annu. Rev. Biochem. 71, 17-50
7. McCann, J., Spingarn, N. E., Kobori, J., and Ames, B. N. (1975) Proc. Natl. Acad. Sci. U.S.A. 72, 979-983
8. Streisinger, G., Okada, Y., Emrich, I., Newton, J., Tsugita, A., Terzaghi, E., and Inouye, M. (1966) Cold Spring Harbor Symp. Quant. Biol. 31, 77-84
9. Potapova, O., Grindley, N. D., and Joyce, C. M. (2002) J. Biol. Chem. 277, 28157-28166
10. Wilson, R. C., and Pata, J. D. (2008) Mol. Cell 29, 767-779
11. Ohashi, E., Bebenek, K., Matsuda, T., Feaver, W. I., Gerlach, V. L., Friedberg, E. C., Ohmori, H., and Kunkel, T. A. (2000) J. Biol. Chem. 275, 39678-39684
12. Wolfle, W. T., Washington, M. T., Prakash, L., and Prakash, S. (2003) Genes Dev. 17, 2191-2199
13. Ling, H., Boudsocq, F., Woodgate, R., and Yang, W. (2004) Mol. Cell 13, 751-762
14. 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
15. Rechkoblit, O., Malinina, L., Cheng, Y., Kuryavyi, V., Broyde, S., Geacintov, N.E., and Patel, D. J. (2006) PLoS Biol. 4, e11
16. Bauer, J., Xing, G, Yagi, H., Sayer, J. M., Jerina, D. M., and Ling, H. (2007) Proc. Natl. Acad. Sci. U.S.A. 104, 14905-14910
17. Eoff, R. L., Stafford, J. B., Szekely, J., Rizzo, C. J., Egli, M., Guengerich, F. P., and Marnett, L. J. (2009) Biochemistry 48, 7079-7088
18. Wang, Y., Musser, S. K., Saleh, S., Marnett, L. J., Egli, M., and Stone, M. P. (2008) Biochemistry 47, 7322-7334
19. Kokoska, R. J., Bebenek, K., Boudsocq, F., Woodgate, R., and Kunkel, T. A. (2002) J. Biol. Chem. 277, 19633-19638
20. Bebenek, K., and Kunkel, T. A. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 4946-4950
21. Ling, H., Boudsocq, F., Woodgate, R., and Yang, W. (2001) Cell 107, 91-102
22. Bloom, L. B., Chen, X., Fygenson, D. K., Turner, J., O'Donnell, M., and Goodman, M. F. (1997) J. Biol. Chem. 272, 27919-27930
23. Efrati, E., Tocco, G., Eritja, R., Wilson, S. H., and Goodman, M. F. (1997) J. Biol. Chem. 272, 2559-2569
24. Kunkel, T. A. (1986) J. Biol. Chem. 261, 13581-13587
25. Kunkel, T. A., and Soni, A. (1988) J. Biol. Chem. 263, 14784-14789
26. Beckman, J. W., Wang, Q., and Guengerich, F. P. (2008) J. Biol. Chem. 283, 36711-36723
27. Borer, P. N. (1975), in Handbook of Biochemistry and Molecular Biology, (Fasman, G. D., ed) 3rd Ed., pp. 589-590, CRC Press, Cleveland, OH
28. Choi, J. Y., Chowdhury, G., Zang, H., Angel, K. C., Vu, C. C., Peterson, L. A., and Guengerich, F. P. (2006) J. Biol. Chem. 281, 38244-38256
29. Zhang, H., Eoff, R. L., Kozekov, I. D., Rizzo, C. J., Egli, M., and Guengerich, F. P. (2009) J. Biol. Chem. 284, 17687-17699
30. Goodman, M. F., Creighton, S., Bloom, L. B., and Petruska, J. (1993) Crit. Rev. Biochem. Mol. Biol. 28, 83-126
31. Zhang, H., Eoff, R. L., Kozekov, I. D., Rizzo, C. J., Egli, M., and Guengerich, F. P. (2009) J. Biol. Chem. 284, 3563-3576
32. Zhang, H., Bren, U., Kozekov, I. D., Rizzo, C. J., Stec, D. F., and Guengerich, F. P. (2009) J. Mol. Biol. 392, 251-269
33. 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
34. Irimia, A., Eoff, R. L., Pallan, P. S., Guengerich, F. P., and Egli, M. (2007) J. Biol. Chem. 282, 36421-36433
35. Tsai, Y. C., and Johnson, K. A. (2006) Biochemistry 45, 9675-9687
36. 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