Effect of Different Divalent Cations on the Kinetics and Fidelity of RB69 DNA Polymerase

Biochemistry

Volumn 55, Issue 18, 2016, Pages 2661-2670

  Vashishtha, Ashwani Kumar ^a   Konigsberg, William H ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; EFFICIENCY; GROUND STATE; METAL IONS; METALS; POLYMERS; POSITIVE IONS;

BASE SELECTIVITY; COFACTORS; DIVALENT CATION; DIVALENT METAL ION; DNA POLYMERASE; EXONUCLEASE ACTIVITY; GROUND-STATE BINDING; TRANSFER REACTION;

CARBON DIOXIDE;

CATION; COBALT; DIVALENT CATION; DNA POLYMERASE; EXONUCLEASE; MAGNESIUM; MANGANESE; METAL ION; NICKEL; NUCLEOTIDE; BACTERIOPHAGE RB69 DNA POLYMERASE; DNA DIRECTED DNA POLYMERASE; PROTEIN BINDING; VIRAL PROTEIN;

ARTICLE; KINETIC PARAMETERS; KINETICS; PRIORITY JOURNAL; BACTERIOPHAGE; BINDING SITE; CHEMISTRY; ENZYMOLOGY; ESCHERICHIA COLI; METABOLISM; VIROLOGY;

BACTERIOPHAGES; BINDING SITES; CATIONS, DIVALENT; COBALT; DNA-DIRECTED DNA POLYMERASE; ESCHERICHIA COLI; MAGNESIUM; MANGANESE; NUCLEOTIDES; PROTEIN BINDING; VIRAL PROTEINS;

EID: 84969706239     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/acs.biochem.5b01350     Document Type: Article

References (28)

1. Drake, J. W. (1969) Comparative rates of spontaneous mutation Nature 221, 1132 10.1038/2211132a0
2. Vaisman, A., Ling, H., Woodgate, R., and Yang, W. (2005) Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis EMBO J. 24, 2957-2967 10.1038/sj.emboj.7600786
3. Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson, S. H., and Kraut, J. (1996) A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta Biochemistry 35, 12762-12777 10.1021/bi9529566
4. Irimia, A., Loukachevitch, L. V., Eoff, R. L., Guengerich, F. P., and Egli, M. (2010) Metal-ion dependence of the active-site conformation of the translesion DNA polymerase Dpo4 from Sulfolobus solfataricus Acta Crystallogr., Sect. F: Struct. Biol. Cryst. Commun. 66, 1013-1018 10.1107/S1744309110029374
5. Irimia, A., Zang, H., Loukachevitch, L. V., Eoff, R. L., Guengerich, F. P., and Egli, M. (2006) Calcium is a cofactor of polymerization but inhibits pyrophosphorolysis by the Sulfolobus solfataricus DNA polymerase Dpo4 Biochemistry 45, 5949-5956 10.1021/bi052511+
6. Xia, S., Wang, M., Blaha, G., Konigsberg, W. H., and Wang, J. (2011) Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase Biochemistry 50, 9114-9124 10.1021/bi201260h
7. Snow, E. T., Xu, L. S., and Kinney, P. L. (1993) Effects of nickel ions on polymerase activity and fidelity during DNA replication in vitro Chem.-Biol. Interact. 88, 155-173 10.1016/0009-2797(93)90089-H
8. Sirover, M. A., Dube, D. K., and Loeb, L. A. (1979) On the fidelity of DNA replication. Metal activation of Escherichia coli DNA polymerase I J. Biol. Chem. 254, 107-111
9. Sirover, M. A. and Loeb, L. A. (1977) On the fidelity of DNA replication. Effect of metal activators during synthesis with avian myeloblastosis virus DNA polymerase J. Biol. Chem. 252, 3605-3610
10. Miyaki, M., Murata, I., Osabe, M., and Ono, T. (1977) Effect of metal cations on misincorporation by E. coli DNA polymerases Biochem. Biophys. Res. Commun. 77, 854-860 10.1016/S0006-291X(77)80056-9
11. Goodman, M. F., Keener, S., Guidotti, S., and Branscomb, E. W. (1983) On the enzymatic basis for mutagenesis by manganese J. Biol. Chem. 258, 3469-3475
12. Vashishtha, A. K. and Kuchta, R. D. (2015) Polymerase and exonuclease activities in herpes simplex virus type 1 DNA polymerase are not highly coordinated Biochemistry 54, 240-249 10.1021/bi500840v
13. Sirover, M. A. and Loeb, L. A. (1976) Infidelity of DNA synthesis in vitro: screening for potential metal mutagens or carcinogens Science 194, 1434-1436 10.1126/science.1006310
14. Wang, C. X., Zakharova, E., Li, J., Joyce, C. M., Wang, J., and Konigsberg, W. (2004) Pre-steady-state kinetics of RB69 DNA polymerase and its exo domain mutants: effect of pH and thiophosphoryl linkages on 3′-5′ exonuclease activity Biochemistry 43, 3853-3861 10.1021/bi0302292
15. Xia, S., Vashishtha, A., Bulkley, D., Eom, S. H., Wang, J., and Konigsberg, W. H. (2012) Contribution of partial charge interactions and base stacking to the efficiency of primer extension at and beyond abasic sites in DNA Biochemistry 51, 4922-4931 10.1021/bi300296q
16. Kuchta, R. D., Mizrahi, V., Benkovic, P. A., Johnson, K. A., and Benkovic, S. J. (1987) Kinetic mechanism of DNA polymerase I (Klenow) Biochemistry 26, 8410-8417 10.1021/bi00399a057
17. Zhang, H., Rhee, C., Bebenek, A., Drake, J. W., Wang, J., and Konigsberg, W. (2006) The L561A substitution in the nascent base-pair binding pocket of RB69 DNA polymerase reduces base discrimination Biochemistry 45, 2211-2220 10.1021/bi052099y
18. Boudsocq, F., Kokoska, R. J., Plosky, B. S., Vaisman, A., Ling, H., Kunkel, T. A., Yang, W., and Woodgate, R. (2004) Investigating the role of the little finger domain of Y-family DNA polymerases in low fidelity synthesis and translesion replication J. Biol. Chem. 279, 32932-32940 10.1074/jbc.M405249200
19. Wang, M., Lee, H. R., and Konigsberg, W. (2009) Effect of A and B metal ion site occupancy on conformational changes in an RB69 DNA polymerase ternary complex Biochemistry 48, 2075-2086 10.1021/bi801627h
20. Wang, T. S., Sedwick, W. D., and Korn, D. (1974) Nuclear deoxyribonucleic acid polymerase. Purification and properties of the homogeneous enzyme from human KB cells J. Biol. Chem. 249, 841-850
21. Seal, G., Shearman, C. W., and Loeb, L. A. (1979) On the fidelity of DNA replication. Studies with human placenta DNA polymerases J. Biol. Chem. 254, 5229-5237
22. Hays, H. and Berdis, A. J. (2002) Manganese substantially alters the dynamics of translesion DNA synthesis Biochemistry 41, 4771-4778 10.1021/bi0120648
23. Villani, G., Tanguy Le Gac, N., Wasungu, L., Burnouf, D., Fuchs, R. P., and Boehmer, P. E. (2002) Effect of manganese on in vitro replication of damaged DNA catalyzed by the herpes simplex virus type-1 DNA polymerase Nucleic Acids Res. 30, 3323-3332 10.1093/nar/gkf463
24. Lee, H. R., Wang, M., and Konigsberg, W. (2009) The reopening rate of the fingers domain is a determinant of base selectivity for RB69 DNA polymerase Biochemistry 48, 2087-2098 10.1021/bi8016284
25. Cotton, F. A., Wilkinson, G., Murillo, C. A., and Bochmann, M. (1999) Advanced Inorganic Chemistry, 6 th ed., John Wiley & Sons, New York.
26. Bock, C. W., Katz, A. K., MArkham, G. D., and Glusker, J. P. (1999) Manganese as a Replacement for Manganese and Zinc: Functional Comparison of the Divalent ions J. Am. Chem. Soc. 121, 7360-7372 10.1021/ja9906960
27. Yu, S. L., Lee, S. K., Johnson, R. E., Prakash, L., and Prakash, S. (2003) The stalling of transcription at abasic sites is highly mutagenic Mol. Cell. Biol. 23, 382-388 10.1128/MCB.23.1.382-388.2003
28. 2+) on in vitro DNA replication by DNA polymerase alpha Cancer Res. 54, 2337-2341