A new paradigm for DNA polymerase specificity

Biochemistry

Volumn 45, Issue 32, 2006, Pages 9675-9687

  Tsai, Yu Chih ^a   Johnson, Kenneth A ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; COMPLEXATION; CONFORMATIONS; DNA; REACTION KINETICS; SUBSTRATES;

CATALYTIC RESIDUES; DEOXYNUCLEOSIDE TRIPHOSPHATE COMPLEXES; KINETIC PARAMETERS; SUBSTRATE DISSOCIATION;

PROTEINS;

AMINO ACID; DNA; DNA POLYMERASE; NUCLEOSIDE TRIPHOSPHATE; T7 DNA POLYMERASE; UNCLASSIFIED DRUG; VIRUS PROTEIN;

AMINO ACID METABOLISM; ARTICLE; BACTERIOPHAGE T7; BASE MISPAIRING; CATALYSIS; CHEMICAL REACTION; CHROMATOPHORE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DISSOCIATION; DNA PROTEIN COMPLEX; ENTHALPY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME BINDING; ENZYME CONFORMATION; ENZYME KINETICS; ENZYME SPECIFICITY; ENZYME STRUCTURE; ENZYME SUBSTRATE; ENZYME SUBSTRATE COMPLEX; FLUORESCENCE; FLUOROPHORE; MOLECULE; NUCLEOTIDE SEQUENCE; POLYMERIZATION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN MOTIF; THERMODYNAMICS;

BACTERIOPHAGE T7; COUMARINS; DNA-DIRECTED DNA POLYMERASE; ENZYME STABILITY; FLUORESCENCE; KINETICS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MUTATION; NUCLEOTIDES; PROTEIN BINDING; SUBSTRATE SPECIFICITY;

EID: 33747462891     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi060993z     Document Type: Article

References (42)

1. Fersht, A. (1998) Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding, W. H. Freeman and Company, New York.
2. Fersht, A. (1985) Enzyme Structure and Mechanism, W. H. Freeman and Company, New York.
3. Fersht, A. R. (1974) Catalysis, binding and enzyme-substrate complementarity, Proc. R. Soc. London, Ser. B 187, 397-407.
4. Post, C. B., and Ray, W. J., Jr. (1995) Re-examination of induced fit as a determinant of substrate specificity in enzymatic reactions, Biochemistry 34, 15881-15885.
5. Johnson, K. A. (1993) Conformational coupling in DNA polymerase fidelity, Annu. Rev. Biochem. 62, 685-713.
6. Joyce, C. M., and Benkovic, S. J. (2004) DNA polymerase fidelity: Kinetics, structure, and checkpoints, Biochemistry 43, 14317-14324.
7. Kornberg, A., and Baker, T. A. (1992) DNA Replication, W. H. Freeman and Company, New York.
8. Goodman, M. F. (1997) Hydrogen bonding revisited: Geometric selection as a principal determinant of DNA replication fidelity, Proc. Natl. Acad. Sci. U.S.A. 94, 10493-10495.
9. Patel, S. S., Wong, I., and Johnson, K. A. (1991) Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutant, Biochemistry 30, 511-525.
10. Wong, I., Patel, S. S., and Johnson, K. A. (1991) An induced-fit kinetic mechanism for DNA replication fidelily-Direct measurement by single-turnover kinetics, Biochemistry 30, 526-537.
11. Mizrahi, V., Henrie, R. N., Marlier, J. F., Johnson, K. A., and Benkovic, S. J. (1985) Rate-limiting steps in the DNA polymerase 1 reaction pathway, Biochemistry 24, 4010-4018.
12. Kali, W. M., Johnson, K. A., Jerva, L. F., and Anderson, K. S. (1992) Mechanism and fidelity of HIV reverse transcriptase, J. Biol. Chem. 267, 25988-25997.
13. Spence, R. A., Kati, W. M., Anderson, K. S., and Johnson, K. A. (1995) Mechanism of inhibition of HIV-1 reverse transcriptase by nonnucleoside inhibitors, Science 267, 988-993.
14. Doublie, S., Tabor, S., Long, A. M., Richardson, C. C., and Ellenberger, T. (1998) Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution, Nature 391, 251-258.
15. Pelletier, H., Sawaya, M. R., Kumar, A., Wilson, S. H., and Kraut, J. (1994) Structures of ternary complexes of rat DNA polymerase β, A DNA template primer, and ddCTP, Science 264, 1891-1903.
16. Sawaya, M. R., Prasad, R., Wilson, S. H., Kraut, J., and Pelletier, H. (1997) Crystal structures of human DNA polymerase β complexed with gapped and nicked DNA: Evidence for an induced fit mechanism, Biochemistry 36, 11205-11215.
17. Huang, H. F., Chopra, R., Verdine, G. L., and Harrison, S. C. (1998) Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: Implications for drug resistance, Science 282, 1669-1675.
18. Patel, P. H., Suzuki, M., Adman, E., Shinkai, A., and Loeb, L. A. (2001) Prokaryotic DNA polymerase 1: Evolution, structure, and "base flipping" mechanism for nucleotide selection, J. Mol. Biol. 308, 823-837.
19. Dunlap, C. A., and Tsai, M. D. (2002) Use of 2-aminopurine and tryptophan fluorescence as probes in kinetic analyses of DNA polymerase β, Biochemistry 41, 11226-11235.
20. Showalter, A. K., and Tsai, M. D. (2002) A reexamination of the nucleotide incorporation fidelity of DNA polymerases, Biochemistry 41, 10571-10576.
21. Rothwell, P. J., Mitaksov, V., and Waksman, G. (2005) Motions of the fingers subdomain of klentaq1 are fast and not rate limiting: Implications for the molecular basis of fidelity in DNA polymerases, Mol. Cell 19, 345-355.
22. Herschlag, D., Piccirilli, J. A., and Cech, T. R. (1991) Ribozyme-catalyzed and nonenzymatic reactions of phosphate diesters: Rate effects upon substitution of sulfur for a nonbridging phosphoryl oxygen atom, Biochemistry 30, 4844-4854.
23. Arndt, J. W., Gong, W. M., Zhong, X. J., 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.
24. Purohit, V., Grindley, N. D. F., and Joyce, C. M. (2003) Use of 2-aminopurine fluorescence to examine conformational changes during nucleotide incorporation by DNA polymerase 1 (Klenow fragment), Biochemistry 42, 10200-10211.
25. Garcia-Diaz, M., Bebenek, K., Gao, G., Pedersen, L. C., London, R. E., and Kunkel, T. A. (2005) Structure-function studies of DNA polymerase lambda, DNA Repair 4, 1358-1367.
26. 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.
27. Lunn, C. A., Kathju, S., Wallace, B. J., Kushner, S. R., and Pigiet, V. (1984) Amplification and purification of plasmid-encoded thioredoxin from Escherichia coli K12, J. Biol. Chem. 259, 469-474.
28. Tsai, Y.-C., Jin, Z., and Johnson, K. A. (2006) Site-specific labeling of T7 DNA polymerase with a conformationally sensitive fluorophore, J. Biol. Chem., manuscript in preparation.
29. Dohno, C., and Saito, I. (2005) Discrimination of single-nucleotide alterations by G-specific fluorescence quenching, ChemBioChem 6, 1075-1081.
30. Florian, J., Goodman, M. F., and Warshel, A. (2005) Computer simulations of protein functions: Searching for the molecular origin of the replication fidelity of DNA polymerases, Proc. Natl. Acad. Sci. U.S.A. 102, 6819-6824.
31. Showalter, A. K., Lamarche, B. J., Bakhtina, M., Su, M. I., Tang, K. H., and Tsai, M. D. (2006) Mechanistic comparison of high-fidelity and error-prone DNA polymerases and ligases involved in DNA repair, Chem. Rev. 106, 340-360.
32. Lee, H., Hanes, J., and Johnson, K. A. (2003) Toxicity of nucleoside analogues used to treat AIDS and the selectivity of the mitochondrial DNA polymerase, Biochemistry 42, 14711-14719.
33. Johnson, K. A. (1995) Rapid quench kinetic analysis of polymerases, adenosine triphosphatases, and enzyme intermediates, Methods Enzymol. 249, 38-61.
34. Johnson, K. A. (1992) Transient-slate kinetic analysis of enzyme reaction pathways, in The Enzymes, pp 1-61, Academic Press, Inc., New York.
35. Beese, L. S., and Steitz, T. A. (1991) Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: A two metal ion mechanism, EMBO J. 10, 25-33.
36. Steitz, T. A., and Steitz, J. A. (1993) A general two-metal-ion mechanism for catalytic RNA, Proc. Natl. Acad. Sci. U.S.A. 90, 6498-6502.
37. Herschlag, D. (1988) The role of induced fit and conformational changes of enzymes in specificity and catalysis, Bioorg. Chem. 16, 62-96.
38. Johnson, S. J., and Beese, L. S. (2004) Structures of mismatch replication errors observed in a DNA polymerase, Cell 116, 803-816.
39. Krahn, J. M., Beard, W. A., and Wilson, S. H. (2004) Structural insights into DNA polymerase β deterrents for misincorporation support an induced-fit mechanism for fidelity, Structure 12, 1823-1832.
40. Brieba, L. G., Eichman, B. F., Kokoska, R. J., Doublie, S., Kunkel, T. A., and Ellenberger, T. (2004) Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase, EMBO J. 23, 3452-3461.
41. Brieba, L. G., Kokoska, R. J., Bebenek, K., Kunkel, T. A., and Ellenberger, T. (2005) A lysine residue in the fingers subdomain of T7 DNA polymerase modulates the miscoding potential of 8-oxo-7,8-dihydroguanosine, Structure 13, 1653-1659.
42. Wolfenden, R. (2003) Thermodynamic and extrathermodynamic requirements of enzyme catalysis, Biophys. Chem. 105, 559-572.