Base excision repair enzyme family portrait: Integrating the structure and chemistry of an entire DNA repair pathway

Structure

Volumn 5, Issue 12, 1997, Pages 1543-1550

  Parikh, Sudip S ^a   Mol, Clifford D ^a   Tainer, John A ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA; ZIZIPHUS MAURITIANA;

EID: 0031574192     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(97)00303-1     Document Type: Review

References (53)

1. Friedberg, E.G., Walker, G.G. & Siede, W. (1995). In DNA Repair and Mutagenesis. ASM Press, Washington DC.
2. Krokan, H.E., Standal, R. & Slupphaug, G. (1997). DNA glycosylases in the base excision repair of DNA. Biochem. J. 325, 1-16.
3. Kubota, Y., Nash, R.A., Klungland, A., Schär, P., Barnes, D.E. & Lindahl, T. (1996). Reconstitution of DNA base excision-repair with purified human proteins: interaction between DNA polymerase β and the XRCC1 protein. EMBO J. 15, 6662-6670.
4. Nicholl, I.D., Nealon, K. & Kenny, M.K. (1997). Reconstitution of human base excision repair with purified proteins. Biochemistry 36, 7557-7566.
5. Matsumoto, Y. & Kim, K. (1995). Excision of deoxyribose phosphate residues by DNA polymerase beta during repair. Science 269, 699-702.
6. Slupphaug, G., Mol, C.D., Kavli, B., Arvai, A.S., Krokan, H.E. & Tainer, J.A. (1996). A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. Nature 384, 87-92.
7. Pelletier, H., Sawaya, M.R., Wolfe, W., Wilson, S.H. & Kraut, J. (1996). Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity. Biochemistry 35, 12742-12761.
8. Caldecott, K.W., Tucker, J.D., Stanker, L.H. & Thompson, L.H. (1995). Characterization of the XRCC1 -DNA ligase III complex in vitro and its absence from mutant hamster cells. Nucleic Acids Res. 23, 4836-4843.
9. Prasad, R., Singhal, R.K., Srivastava, D.K., Molina, J.T., Tomkinson, A.E. & Wilson, S.H. (1996). Specific interaction of DNA polymerase β and DNA ligase I in a multiprotein base excision repair complex from bovine testis. J. Biol. Chem. 271, 16000-16007.
10. Bennett, R.A.O., Wilson, D.M. III, Wong, D. & Demple, B. (1997). Interaction of human apurinic endonuclease and DNA polymerase β in the base excision repair pathway. Proc. Natl. Acad. Sci. USA 94, 7166-7169.
11. Frosina, G., et al., & Dogliotti, E. (1996). Two pathways for base excision repair in mammalian cells. J. Biol. Chem. 271, 9573-9578.
12. 2. Tainer, J.A., Thayer, M.M. & Cunningham, R.P. (1995). DNA repair proteins. Curr. Opin. Struct. Biol. 5, 20-26.
13. Cunningham, R.P. (1997). DNA glycosylates. Mutat. Res. 383, 189-196.
14. Lindahl, T. & Nyberg, B. (1974). Heat-induced deamination of cytosine residues in deoxyribonucleic acid. Biochemistry 13, 3405-3410.
15. Mol, C.D., et al., & Tainer, J.A. (1995). Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis. Cell 80, 869-878.
16. Savva, R., McAuley-Hecht, K., Brown, T. & Pearl, L. (1995). The structural basis of specific base-excision repair by uracil-DNA glycosylase. Nature 373, 487-493.
17. Kavli, B., et al., & Krokan, H.E. (1996). Excision of cytosine and thymine from DNA by mutants of human uracil-DNA glycosylase. EMBO J. 15, 3442-3447.
18. Kuo, C.F., McRee, D.E., Fisher, C.L., O'Handley, S.F., Cunningham, R.P. & Tainer, J.A. (1994). Atomic structure of the DNA repair [4Fe-4S] enzyme endonuclease III. Science 258, 434-440.
19. Thayer, M.M., Ahern, H., Xing, D., Cunningham, R.P. & Tainer, J.A. (1995). Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure. EMBO J. 14, 4108-4120.
20. Nash, H.M., et al., & Verdine, G.L (1996). Cloning of a yeast 8-oxoguanine DNA glycosylase reveals the existence of a base-excision DNA-repair protein superfamily. Curr. Biol. 6, 968-980.
21. Doherty, A.J., Serpell, L.C. & Ponting, C.P. (1996). The helix-hairpinhelix DNA-binding motif: a structural basis for non-sequence specific recognition of DNA. Nucleic Acids Res. 24, 2488-2497.
22. Labahn, J., Scharer, O.D., Long, A., Ezaz-Nikpay, K., Verdie, G.L. & Ellenberger, T.E. (1996). Structural basis for the excision repair of alkylation-damaged DNA. Cell 86, 321-329.
23. Yamagata, Y., et al., & Fujii, S. (1996). Three-dimensional structure of a DNA repair enzyme, 3-methyladenine DNA glycosylase II, from Escherichia coli. Cell 86, 311-319.
24. Nash, H.M., Lu, R., Lane, W.S. & Verdine, G.L. (1997). The critical active-site amine of the human 8-oxoguanine DNA glycosylase, hOgg1: direct identification, ablation and chemical reconstitution. Chem. Biol. 4, 693-702.
25. Dodson, M.L., Michaels, M.L. & Lloyd, R.S. (1994). Unified catalytic mechanism for DNA glycosylases. J. Biol. Chem. 269, 32709-32712.
26. Mol, C.D., Kuo, C.-F., Thayer, M.M., Cunningham, R.P. & Tainer, J.A. (1995). Structure and function of the multifunctional DNA-repair enzyme exonuclease III. Nature 374, 381-386.
27. Gorman, M.A., et al., & Freemont, P.S. (1997). The crystal structure of the human DNA repair endonuclease HAP1 suggests the recognition of extra-helical deoxyribose at DNA abasic sites. EMBO J. 16, 6548-6558.
28. Xanthoudakis, S., Miao, G., Wang, F., Pan, Y.-C.E. & Curran, T. (1992). Redox activation of Fos-Jun DNA binding activity is mediated by a DNA repair enzyme. EMBO J. 11, 3323-3335.
29. Fent, Q., Moran, J.V., Kazizian, H.H., Jr. & Boeke, J.D. (1996). Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87, 905-916.
30. Lahm, A. & Suck, D. (1991). DNase I-induced DNA conformation. 2 Å structure of a DNase I-octamer complex. J. Mol. Biol. 222, 645-667.
31. Weston, S.A., Lahm, A. & Suck, D. (1992). X-ray structure of the DNase l-d(GGTATACC)2 complex at 2.3 Å resolution. J. Mol. Biol. 226, 1237-1256.
32. Wilson, D.M., III, Takeshita, M., Grollman, A.P. & Demple, B. (1995). Incision activity of human apurinic endonuclease (Ape) at abasic site analogs in DNA. J. Biol. Chem. 270, 16002-16007.
33. Wilson, D.M., III, Takeshita, M. & Demple, B. (1997). Abasic site binding by the human apurinic endonuclease, Ape, and determination of the DNA contact sites. Nucleic Acids Res. 25, 933-939.
34. 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.
35. Pelletier, H., Sawaya, M.R., Kumar, A., Wilson, S.H. & Kraut, J. (1994). Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP. Science 264, 1891-1903.
36. Davies, J.F., II, Almassy, R.J., Hostomska, Z., Ferre, R.A. & Hostomsky, Z. (1994). 2.3 Å crystal structure of the catalytic domain of DNA polymerase beta. Cell 76, 1123-1133.
37. Sawaya, M.R., Prasad, R., Wilson, S.H., Kraut, J. & Pelletier, H. (1997). Crystal structure of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism. Biochemistry 36, 11205-11215.
38. Freemont, P.S., Friedman, J.M., Beese, L.S., Sanderson, M.R. & Steitz, T.A. (1988). Cocrystal structure of an editing complex of Klenow fragment with DNA. Proc. Natl. Acad. Sci. USA 85, 8924-8928.
39. Kim, Y., Eom, S.H., Wang, J, Lee, D.S., Suh, S.W. & Steitz, T.A. (1995). Crystal structure of Thermus aquaticus DNA polymerase. Nature 376, 612-616.
40. Sobol, R.W., et al., & Wilson, S.H. (1996). Requirement of mammalian DNA polymerase β in base-excision repair. Nature 379, 183-186.
41. Pelletier, H. & Sawaya, M.R. (1996). Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis. Biochemistry 35, 12778-12787.
42. Pelletier, H., Sawaya, M.R., Wolfie, W., Wilson, S.H. & Kraut, J. (1996). A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta. Biochemistry 35, 12762-12777.
43. Zhong, X., Patel, S.S., Werneburg, B.G. & Tsai, M.D. (1997). DNA polymerase beta: multiple conformational changes in the mechanism of catalysis. Biochemistry 36, 11891-11900.
44. Kiefer, J.R., et al., & Beese, L.S. (1997). Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 Å. Structure 5, 95-108.
45. Beese, L.S., Derbyshire, V. & Steitz, T.A. (1993). Structure of DNA polymerase I Klenow fragment bound to duplex DNA. Science 260, 352-355.
46. Joyce, C.M. & Steitz, T.A. (1994). Function and structure relationships in DNA polymerases. Annu. Rev. Biochem. 63, 777-822.
47. Lehman, I.R. (1974). DNA ligase: structure, mechanism, and function. Science 186, 790-797.
48. Hakansson, K., Doherty, A.J., Shuman, S. & Wigley, D.B. (1997). X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzyme. Cell 89, 545-553.
49. Nash, R.A., Caldecott, K.W., Barnes, D.E. & Lindahl, T. (1997). XRCC1 protein interacts with one of two distinct forms of DNA ligase III. Biochemistry 36, 5207-5211.
50. Shuman, S. (1996). Closing the gap on DNA ligase. Structure 4, 653-656.
51. Subramanya, H.S., Doherty, A.J., Ashford, S.R. & Wigley, D.B. (1996). Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7. Cell 85, 607-615.
52. Wlassoff, W.A., Dymshits, G.M. & Lavrik, O.I. (1996). A model for DNA polymerase translocation: worm-like movement of DNA within the binding cleft. FEBS Lett. 390, 6-9.
53. Hughes, S.H., Hostomsky, Z., LeGrice, S.F., Lentz, K. & Arnold, E. (1996). What is the orientation of DNA polymerases on their templates? J. Virology 70, 2679-2683.