How DNA polymerases catalyze DNA replication, repair, and mutation

Biochemistry

Volumn 53, Issue 17, 2014, Pages 2749-2751

  Tsai, Ming Daw ^a,b  

^a INSTITUTE OF BIOLOGICAL CHEMISTRY   (Taiwan)

^b NATIONAL TAIWAN UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE; DOUBLE STRANDED DNA;

AFRICAN SWINE FEVER VIRUS; ARTICLE; BASE PAIRING; CATALYSIS; CONFORMATION; DNA REPAIR; DNA REPLICATION; DNA STRUCTURE; DNA SYNTHESIS; ENERGY TRANSFER; ENZYME ACTIVE SITE; GENE MUTATION; GEOBACILLUS STEAROTHERMOPHILUS; HYDROGEN BOND; NONHUMAN; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; X RAY CRYSTALLOGRAPHY;

CATALYTIC DOMAIN; DNA REPAIR; DNA REPLICATION; DNA-DIRECTED DNA POLYMERASE; MUTATION; SUBSTRATE SPECIFICITY;

EID: 84899803441     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi500417m     Document Type: Article

References (33)

1. Xia, S. and Konigsberg, W. (2014) RB69 DNA Polymerase Structure, Kinetics, and Fidelity Biochemistry DOI: 10.1021/bi4014215
2. Beard, W. A. and Wilson, S. H. (2014) Structure and Mechanism of DNA Polymerase β Biochemistry DOI: 10.1021/bi500139h
3. Bebenek, K., Pedersen, L. C., and Kunkel, T. A. (2014) Structure-Function Studies of DNA Polymerase λ Biochemistry DOI: 10.1021/bi4017236
4. Yang, W. (2014) A Summary of Y-Family DNA Polymerases and a Case Study of Human DNA Polymerase π Biochemistry DOI: 10.1021/bi500019s
5. Maxwell, B. A. and Suo, Z. (2014) Recent Insight into the Kinetic Mechanisms and Conformational Dynamics of Y-Family DNA Polymerases Biochemistry DOI: 10.1021/bi5000405
6. Hubscher, U., Spadari, S., Villani, G., and Maga, G. (2010) DNA Polymerases: Discovery, Characterization, and Functions in Cellular DNA Transactions, 1st ed., World Scientific Publishing Co., Singapore.
7. Goodman, M. F. and Tippin, B. (2000) The expanding polymerase universe Nat. Rev. Mol. Cell Biol. 1, 101-109
8. Showalter, A. K., Byeon, I. J., Su, M. I., and Tsai, M. D. (2001) Solution structure of a viral DNA polymerase X and evidence for a mutagenic function Nat. Struct. Biol. 8, 942-946
9. Maciejewski, M. W., Shin, R., Pan, B., Marintchev, A., Denninger, A., Mullen, M. A., Chen, K., Gryk, M. R., and Mullen, G. P. (2001) Solution structure of a viral DNA repair polymerase Nat. Struct. Biol. 8, 936-941
10. Kool, E. T. and Sintim, H. O. (2006) The difluorotoluene debate: A decade later Chem. Commun. 3665-3675
11. Lee, H. R., Helquist, S. A., Kool, E. T., and Johnson, K. A. (2008) Importance of Hydrogen Bonding for Efficiency and Specificity of the Human Mitochondrial DNA Polymerase J. Biol. Chem. 283, 14402-14410
12. Betz, K., Malyshev, D. A., Lavergne, T., Welte, W., Diederichs, K., Dwyer, T. J., Ordoukhanian, P., Romesberg, F. E., and Marx, A. (2012) Structural Insights into DNA Replication without Hydrogen Bonds A. Nat. Chem. Biol. 8, 612-614
13. Johnson, K. A. (1993) Conformational Coupling in DNA Polymerase Fidelity Annu. Rev. Biochem. 62, 685-713
14. Arndt, J. W., Gong, W., Zhong, X., Showalter, A. K., Liu, J., Dunlap, C. A., Lin, Z., Paxson, C., Tsai, M.-D., and Chan, M. K. (2001) Insight into the Catalytic Mechanism of DNA Polymerase β: Structures of Intermediate Complexes Biochemistry 40, 5368-5375
15. Moon, A. F., Pryor, J. M., Ramsden, D. A., Kunkel, T. A., Bebenek, K., and Pedersen, L. C. (2014) Sustained active site rigidity during synthesis by human DNA polymerase μ Nat. Struct. Mol. Biol. 21, 253-260
16. Zhou, B.-L., Pata, J. D., and Steitz, T. A. (2001) Crystal Structure of a DinB Lesion Bypass DNA Polymerase Catalytic Fragment Reveals a Classic Polymerase Catalytic Domain Mol. Cell 8, 427-437
17. Garcia-Diaz, M., Bebenek, K., Krahn, J. M., Kunkel, T. A., and Pedersen, L. C. (2005) A closed conformation for the Pol λ catalytic cycle Nat. Struct. Mol. Biol. 12, 97-98
18. Bermek, O., Grindley, N. D. F., and Joyce, C. M. (2013) Prechemistry Nucleotide Selection Checkpoints in the Reaction Pathway of DNA Polymerase I and Roles of Glu710 and Tyr766 Biochemistry 52, 6258-6274
19. Hohlbein, J., Aigrain, L., Craggs, T. D., Bermek, O., Potapova, O., Shoolizadeh, P., Grindley, N. D., Joyce, C. M., and Kapanidis, A. N. (2013) Conformational landscapes of DNA polymerase λ and mutator derivatives establish fidelity checkpoints for nucleotide insertion Nat. Commun. 4, 2131
20. Brenlla, A., Markiewicz, R. P., Rueda, D., and Romano, L. J. (2014) Nucleotide selection by the Y-family DNA polymerase Dpo4 involves template translocation and misalignment Nucleic Acids Res. 42, 2555-2563
21. Schlick, T., Arora, K., Beard, W. A., and Wilson, S. H. (2012) Perspective: pre-chemistry conformational changes in DNA polymerase mechanisms Theor. Chem. Acc. 131, 1287
22. Ram Prasad, B., Kamerlin, S. C. L., Florián, J., and Warshel, A. (2012) Prechemistry barriers and checkpoints do not contribute to fidelity and catalysis as long as they are not rate limiting Theor. Chem. Acc. 131, 1288
23. Olson, A. C., Patro, J. N., Urban, M., and Kuchta, R. D. (2013) The Energetic Difference between Synthesis of Correct and Incorrect Base Pairs Accounts for Highly Accurate DNA Replication J. Am. Chem. Soc. 135, 1205-1208
24. Oertell, K., Chamberlain, B. T., Wu, Y., Ferri, E., Kashemirov, B. A., Beard, W. A., Wilson, S. H., McKenna, C. E., and Goodman, M. F. (2014) Transition State in DNA Polymerase β Catalysis: Rate-Limiting Chemistry Altered by Base-Pair Configuration Biochemistry 53, 1842-1848
25. Showalter, A. K. and Tsai, M.-D. (2002) A Reexamination of the Nucleotide Incorporation Fidelity of DNA Polymerases Biochemistry 41, 10571-10576
26. Luo, G., Wang, M., Konigsberg, W. H., and Xie, X. S. (2007) Single-molecule and ensemble fluorescence assays for a functionally important conformational change in T7 DNA polymerase Proc. Natl. Acad. Sci. U.S.A. 104, 12610-12615
27. Sampoli Benítez, B. A., Arora, K., Balistreri, L., and Schlick, T. (2008) Mismatched Base-Pair Simulations for ASFV Pol X/DNA Complexes Help Interpret Frequent G·G Misincorporation J. Mol. Biol. 384, 1086-1097
28. Tang, K.-H., Niebuhr, M., Tung, C.-S., Chan, H.-c., Chou, C.-C., and Tsai, M.-D. (2008) Mismatched dNTP incorporation by DNA polymerase β does not proceed via globally different conformational pathways Nucleic Acids Res. 36, 2948-2957
29. Bebenek, K., Pedersen, L. C., and Kunkel, T. A. (2011) Replication infidelity via a mismatch with Watson-Crick geometry Proc. Natl. Acad. Sci. U.S.A. 108, 1862-1867
30. Xia, S., Wang, J., and Konigsberg, W. H. (2013) DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase J. Am. Chem. Soc. 135, 193-202
31. Wang, W., Hellinga, H. W., and Beese, L. S. (2011) Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis Proc. Natl. Acad. Sci. U.S.A. 108, 17644-17648
32. Wu, W.-J., Su, M.-I., Wu, J.-L., Kumar, S., Lim, L.-h., Wang, C.-W. E., Nelissen, F. H. T., Chen, M.-C. C., Doreleijers, J. F., Wijmenga, S. S., and Tsai, M.-D. (2014) How a Low-Fidelity DNA Polymerase Chooses Non-Watson-Crick from Watson-Crick Incorporation J. Am. Chem. Soc. 136, 4927-4937
33. Showalter, A. K. and Tsai, M.-D. (2001) A DNA Polymerase with Specificity for Five Base Pairs J. Am. Chem. Soc. 123, 1776-1777