Structural insights into DNA polymerase β fidelity: Hold tight if you want it right

Chemistry and Biology

Volumn 5, Issue 1, 1998, Pages R7-

  Beard, William A ^a   Wilson, Samuel H ^a  

^a NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0031883128     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/s1074-5521(98)90081-3     Document Type: Short Survey

References (27)

1. Lindahl, T. (1993). Instability and decay of the primary structure of DNA. Nature 362, 709-715.
2. Pelletier, H., Sawaya, M.R., Kumar, A., Wilson, S.H. & Kraut, J. (1994). Structures of ternary complexes of rat DNA polymerase β, a DNA template-primer, and ddCTP. Science 264, 1891-1903.
3. Beard, W.A. & Wilson, S.H. (1995). Purification and domain-mapping of mammalian DNA polymerase β. Methods Enzymel. 262, 98-107.
4. Pelletier, H., Sawaya, M.R., Wolfle, W., Wilson, S.H. & Kraut, J. (1996). Crystal structures of human DNA polymerase β complexed with DNA: implications for catalytic mechanism, processivity, and fidelity. Biochemistry 35, 12742-12761.
5. Sawaya, M.R., Prasad, P., Wilson, S.H., Kraut, J. & 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.
6. Kunkel, T.A. (1992). DNA replication fidelity. J. Biol. Chem. 267, 18251-18254.
7. Kunkel, T.A. (1985), The mutational specificity of DNA polymerase-β during in vitro DNA synthesis: production of frameshift, base substitution, and deletion mutations. J. Biol. Chem. 260, 5787-5796.
8. Petruska, J., Goodman, M.F., Boosalis, M.S., Sowers, L.C., Cheong, C. & Tinoco, I., Jr. (1988). Comparison between DNA melting thermodynamics and DNA polymerase fidelity. Proc. Natl Acad. Sci, USA 85, 6252-6256.
9. Efrati, E., Tocco, G., Eritja, R., Wilson, S.H. & Goodman, M.F. (1997). Abasic translesion synthesis by DNA polymerase beta violates the 'A-rule' - novel types of nucleotide incorporation by human DNA polymerase beta at an abasic lesion in different sequence contexts. J. Biol. Chem. 272, 2559-2569.
10. Hashim, M.F., Schnetzboutaud, N. & Marnett, L.J. (1997). Replication of template-primers containing propanodeoxyguanosine by DNA polymerase β: Induction of base pair substitution and frameshift mutations by template slippage and deoxynucleoside triphosphate stabilization. J. Biol. Chem. 272, 20205-20212.
11. Matsumoto, Y. & Kim, K. (1995). Excision of deoxyribose phosphate residues by DNA polymerase β during DNA repair. Science 269, 699-702.
12. Prasad, R., Beard, W.A. & Wilson, S.H. (1994). Studies of gapped DNA substrate binding by mammalian DNA polymerase β: Dependence on 5′-phosphate group. J. Biol. Chem. 269, 18096-18101.
13. Beard, W.A., et al., & Wilson, S.H. (1996). Enzyme-DNA interactions required for efficient nucleotide incorporation and discrimination in human DNA polymerase β. J. Biol. Chem. 271, 12141-12144.
14. Chagovetz, A.M., Sweasy, J.B. & Preston, B.D. (1997). Increased activity and fidelity of DNA polymerase β on single-nucleotide gapped DNA. J. Biol. Chem. 272, 27501-27504.
15. Lavrik, O.I., et al., & Wilson, S.H. (1996). dNTP binding to HIV-1 reverse transcriptase and mammalian DNA polymerase β as revealed by affinity labeling with a photoreactive dNTP analog. J. Biol. Chem. 271, 21891-21897.
16. Echols, H. & Goodman, M.F. (1991). Fidelity mechanisms in DNA replication. Annu. Rev. Biochem. 60, 477-511.
17. Goodman, M.F. (1997). Hydrogen bonding revisited: Geometric selection as a principal determinant of DNA replication fidelity. Proc. Natl Acad. Sci. USA 94, 10493-10495.
18. Moran, S., Ren, R.X.-F. & Kool, E.T. (1997). A thymidine triphosphate shape analog lacking Watson-Crick pairing ability is replicated with high sequence selectivity. Proc. Natl Acad. Sci. USA 94, 10506-10511.
19. Sawaya, M.R., Pelletier, H., Kumar, A., Wilson, S.H. & Kraut, J. (1994). Crystal structure of rat DNA polymerase β: evidence for a common polymerase mechanism. Science 264, 1930-1935.
20. Joyce, C.M. (1997). Choosing the right sugar: how polymerases select a nucleotide substrate. Proc. Natl Acad. Sci. USA 94, 1619-1622.
21. Ahn, J., Werneburg, B.G. & Tsai, M.D. (1997). DNA polymerase β: structure-fidelity relationship from pre-steady-state kinetic analyses of all possible correct and incorrect base pairs for wild type and R283A mutant. Biochemistry 36, 1100-1107.
22. Washington, S.L., et al., & Sweasy, J.B. (1997). A genetic system to identify DNA polymerase β mutator mutants. Proc. Natl Acad. Sci. USA 94, 1321-1326.
23. Johnson, K.A. (1993). Conformational coupling in DNA polymerase fidelity. Annu. Rev. Biochem. 62, 685-713.
24. Kraynov, V.S., Werneburg, B.G., Zhong, X.J., Lee, H., Ahn, J.W. & Tsai, M.D. (1997). DNA polymerase β: analysis of the contributions of tyrosine-271 and asparagine-279 to substrate specificity and fidelity of DNA replication by pre-steady-state kinetics. Biochem. J. 323, 103-111.
25. Bebenek, K., et al., & Kunkel, T.A. (1997). A minor groove binding track in reverse transcriptase. Nat. Struct. Biol. 3, 194-197.
26. Nicholls, A., Sharp, K.A. & Honig, B. (1991). Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281-296.
27. Hunter, W.N., Brown, T., Kneale, G., Anand, N.N., Rabinovich, D. & Kennard, O. (1987). The structure of guanosine-thymidine mismatches in B-DNA at 2.5-Å resolution. J. Biol. Chem. 262, 9962-9970.