Initiation of base excision repair: Glycosylase mechanisms and structures

Annual Review of Biochemistry

Volumn 68, Issue , 1999, Pages 255-285

  McCullough, Amanda K ^a   Dodson, M L ^a   Lloyd, R Stephen ^a  

^a UNIVERSITY OF TEXAS MEDICAL BRANCH   (United States)

Author keywords

Alkylation DNA damage; AP lyase; Base flipping; Oxidative DNA damage; Ultraviolet light DNA damage

Indexed keywords

DNA (APURINIC OR APYRIMIDINIC SITE) LYASE; DNA GLYCOSYLTRANSFERASE; LYASE;

ALKYLATION; CATALYSIS; CRYSTAL STRUCTURE; DNA BINDING; DNA DAMAGE; ENZYME CONFORMATION; ENZYME MECHANISM; EXCISION REPAIR; OXIDATION; OXIDATIVE STRESS; PRIORITY JOURNAL; REVIEW; STEREOCHEMISTRY; ULTRAVIOLET RADIATION;

CATALYSIS; DNA DAMAGE; DNA GLYCOSYLASES; DNA REPAIR; N-GLYCOSYL HYDROLASES; PROTEIN CONFORMATION;

EID: 0032836651     PISSN: 00664154     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.biochem.68.1.255     Document Type: Review

References (173)

1. Friedberg EC, Walker GC, Siede W. 1995. DNA Repair and Mutagenesis. Washington, DC: Am. Soc. Microbiol.
2. Fishel R. 1998. Genes Dev. 12:2096-101
3. Jiricny J. 1996. Cancer Surv. 28:47-68
4. Kolodner R. 1996. Genes Dev. 10:1433-42
5. Lehmann AR. 1998. BioEssays 20:146-55
6. Modrich P, Lahue R. 1996. Annu. Rev. Biochem. 65:101-33
7. Modrich P. 1997. J. Biol. Chem. 272:24727-30
8. Wood RD. 1996. Annu. Rev. Biochem. 65:135-67
9. Wood RD. 1997. J. Biol. Chem. 272:23465-68
10. Basu AK, Essigmann JM. 1995. In DNA Repair Mechanisms, ed. JM Vos, pp. 1-24. Austin, TX: Landes
11. Singer B, Hang B. 1997. Chem. Res. Toxicol. 10:713-32
12. Cunningham RP. 1997. Mutat. Res. 383:189-96
13. Lindahl T, Karran P, Wood RD. 1997. Curr. Opin. Genet. Dev. 7:158-69
14. Mitra S, Hazra TK, Roy R, Ikeda S, Biswas T, et al. 1997. Mol. Cells 7:305-12
15. Wilson SH. 1998. Mutat. Res. 407:203-15
16. Parikh SS, Mol CD, Tainer JA. 1997. Structure 5:1543-50
17. Krokan HE, Standal R, Slupphaug G. 1997. Biochem. J. 325:1-16
18. Vassylyev DG, Morikawa K. 1997. Curr. Opin. Struct. Biol. 7:103-9
19. Sun B, Latham KA, Dodson ML, Lloyd RS. 1995. J. Biol. Chem. 270:19501-8
20. Nakabeppu Y, Sekiguchi M. 1981. Proc. Natl. Acad. Sci. USA 78:2742-46
21. Dodson ML, Schrock RD, Lloyd RS. 1993. Biochemistry 32:8284-90
22. Dodson ML, Michaels ML, Lloyd RS. 1994. J. Biol. Chem. 269:32709-12
23. Cadet J, Tcoule R. 1974. J. Am. Chem. Soc. 96:6517-19
24. Kelley JA, Driscoll JS, McCormack JJ, Roth JS, Marquez VE. 1986. J. Med. Chem. 29:2351-58
25. Gerlt JA. 1993. In Nucleases, ed. SM Linn, RS Lloyd, RJ Roberts, pp. 1-34. Plainview/Cold Spring Harbor, NY: Cold Spring Harbor Lab.
26. Purmal AA, Rabow LE, Lampman GW, Cunningham RP, Kow YW. 1996. Mutat. Res. 364:193-207
27. Parikh SS, Mol CD, Slupphaug G, Bharati S, Krokan HE, Tainer JA. 1998. EMBO J. 17:5214-26
28. Mazumder A, Gerlt JA, Rabow L, Absalon MJ, Stubbe J, Bolton P. 1989. J. Am. Chem. Soc. 111:8029
29. Mazumder A, Gerlt JA, Absalon MJ, Stubbe J, Cunningham RP, et al. 1991. Biochemistry 30:1119-26
30. Vassylyev DG, Kashiwagi T, Mikami Y, Ariyoshi M, Iwai S, et al. 1995. Cell 83:773-82
31. Barrett TE, Savva R, Panayotou G, Barlow T, Brown T, et al. 1998. Cell 92:117-29
32. Mitchell DL. 1988. Photochem. Photobiol. 48:51-57
33. Lloyd RS. 1998. Prog. Nucleic Acid Res. 62:155-75
34. Lloyd RS. 1998. Mutat. Res. 408:159-70
35. Smith CA, Taylor JS. 1993. J. Biol. Chem. 268:11143-51
36. Dizdaroglu M, Zastawny TH, Carmical JR, Lloyd RS. 1996. Mutat. Res. 362:1-8
37. Piersen CE, Prince MA, Augustine ML, Dodson ML, Lloyd RS. 1995. J. Biol. Chem. 270:23475-84
38. Shiota S, Nakayama H. 1997. Proc. Natl. Acad. Sci. USA 94:593-98
39. Furuta M, Schrader JO, Schrader HS, Kokjohn TA, Nyaga S, et al. 1997. Appl. Environ. Microbiol. 63:1551-56
40. McCullough AK, Romberg MT, Nyaga S, Wei Y, Wood TG, et al. 1998. J. Biol. Chem. 273:13136-42
41. Morikawa K, Matsumoto O, Tsujimoto M, Katayanagi K, Ariyoshi M, et al. 1992. Science 256:523-26
42. Morikawa K, Ariyoshi M, Vassylyev DG, Matsumoto O, Katayanagi K, Ohtsuka E. 1995. J. Mol. Biol. 249:360-75
43. McCullough AK, Schärer O, Verdine GL, Lloyd RS. 1996. J. Biol. Chem. 271:32147-52
44. Mol CD, Arvai AS, Slupphaug G, Kavli B, Alseth I, et al. 1995. Cell 80:869-78
45. Savva R, McAuley-Hecht K, Brown T, Pearl L. 1995. Nature 373:487-93
46. Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA. 1996. Nature 384:87-92
47. Impellizzeri KJ, Anderson B, Burgers PM. 1991. J. Bacteriol. 173:6807-10
48. Krokan H, Wittwer CU. 1981. Nucleic Acids Res. 9:2599-613
49. Delort AM, Duplaa AM, Molko D, Teoule R, Leblanc JP, Laval J. 1985. Nucleic Acids Res. 13:319-35
50. Dizdaroglu M, Karakaya A, Jaruga P, Slupphaug G, Krokan HE. 1996. Nucleic Acids Res. 24:418-22
51. Mauro DJ, De Riel JK, Tallarida RJ, Sirover MA. 1993. Mol. Pharmacol. 43:854-57
52. Zastawny TH, Doetsch PW, Dizdaroglu M. 1995. FEBS Lett. 364:255-58
53. Hatahet Z, Kow YW, Purmal AA, Cunningham RP, Wallace SS. 1994. J. Biol. Chem. 269:18814-20
54. Mol CD, Arvai AS, Sanderson RJ, Slupphaug G, Kavli B, et al. 1995. Cell 82:701-8
55. Kavli B, Slupphaug G, Mol CD, Arvai AS, Peterson SB, et al. 1996. EMBO J. 15:3442-47
56. Riggs AD, Jones PA. 1983. Adv. Cancer Res. 40:1-30
57. Brown TC, Jiricny J. 1987. Cell 50:945-50
58. Wiebauer K, Jiricny J. 1989. Nature 339:234-36
59. Wiebauer K, Jiricny J. 1990. Proc. Natl. Acad. Sci. USA 87:5842-45
60. Neddermann P, Gallinari P, Lettieri T, Schmid D, Truong O, et al. 1996. J. Biol. Chem. 271:12767-74
61. Neddermann P, Jiricny J. 1993. J. Biol. Chem. 268:21218-24
62. Neddermann P, Jiricny J. 1994. Proc. Natl. Acad. Sci. USA 91:1642-46
63. Gallinari P, Jiricny J. 1996. Nature 383:735-38
64. Ames BN, Gold LS. 1991. Mutat. Res. 250:3-16
65. Breimer LH. 1990. Mol. Carcinog. 3:188-97
66. Demple B, Harrison L. 1994. Annu. Rev. Biochem. 63:915-48
67. Wallace SS. 1994. Int. J. Radiat. Biol. 66:579-89
68. Dizdaroglu M, Laval J, Boiteux S. 1993. Biochemistry 32:12105-11
69. Hilbert TP, Chaung W, Boorstein RJ, Cunningham RP, Teebor GW. 1997. J. Biol. Chem. 272:6733-40
70. Aspinwall R, Rothwell DG, Roldan-Arjona T, Anselmino C, Ward CJ, et al. 1997. Proc. Natl. Acad. Sci. USA 94:109-14
71. Eide L, Bjoras M, Pirovano M, Alseth I, Berdal KG, Seeberg E. 1996. Proc. Natl. Acad. Sci. USA 93:10735-40
72. You HJ, Swanson RL, Doetsch PW. 1998. Biochemistry 37:6033-40
73. O'Handley S, Scholes CP, Cunningham RP. 1995. Biochemistry 34:2528-36
74. Melamede RJ, Hatahet Z, Kow YW, Ide H, Wallace SS. 1994. Biochemistry 33:1255-64
75. Jiang D, Hatahet Z, Melamede RJ, Kow YW, Wallace SS. 1997. J. Biol. Chem. 272:32230-39
76. Jiang D, Hatahet Z, Blaisdell JO, Melamede RJ, Wallace SS. 1997. J. Bacteriol. 179:3773-82
77. Kuo CF, McRee DE, Fisher CL, O'Handley SF, Cunningham RP, Tainer JA. 1992. Science 258:434-40
78. Thayer MM, Ahern H, Xing D, Cunningham RP, Tainer JA. 1995. EMBO J. 14:4108-20
79. Doherty AJ, Serpell LC, Ponting CP. 1996. Nucleic Acids Res. 24:2488-97
80. Kao JY, Goljer I, Phan TA, Bolton PH. 1993. J. Biol. Chem. 268:17787-93
81. Kung HC, Bolton PH. 1997, J. Biol. Chem. 272:9227-36
82. Rydberg B, Lindahl T. 1982. EMBO J. 1:211-16
83. Singer B, Kusmierek JT. 1982. Annu. Rev. Biochem. 51:655-93
84. Lloyd RS, Linn SM. 1993. In Nucleases, ed. SM Linn, RS Lloyd, RJ Roberts, pp. 263-316. Plainview/Cold Spring Harbor, NY: Cold Spring Harbor Lab.
85. Karran P, Lindahi T, Ofsteng I, Evensen GB, Seeberg E. 1980. J. Mol. Biol. 140:101-27
86. Hickson ID. 1997. Base Excision Repair of DNA Damage. Georgetown. TX: Landes BioSci.
87. Dosanjh MK, Roy R, Mitra S, Singer B. 1994. Biochemistry 33:1624-28
88. Saparbaev M, Kleibl K, Laval J. 1995. Nucleic Acids Res. 23:3750-55
89. Habraken Y, Carter CA, Kirk MC, Ludlum DB. 1991. Cancer Res. 51:499-503
90. Matijasevic Z, Sekiguchi M, Ludlum DB. 1992. Proc. Natl. Acad. Sci. USA 89:9331-34
91. Bjelland S, Birkeland NK, Benneche T, Volden G, Seeberg E. 1994. J. Biol. Chem. 269:30489-95
92. Bjelland S, Eide L, Time RW, Stote R, Eftedal I, et al. 1995. Biochemistry 34:14758-64
93. Bjoras M, Klungland A, Johansen RF, Seeberg E. 1995. Biochemistry 34:4577-82
94. Schärer OD, Ortholand JY, Ganesan A, Ezaz-Nikpay K, Verdine GL. 1995. J. Am. Chem. Soc. 117:6623-24
95. Labahn J, Schärer OD, Long A, Ezaz-Nikpay K, Verdine GL, Ellenberger TE. 1996. Cell 86:321-29
96. Yamagata Y, Kato M, Odawara K, Tokuno Y, Nakashima Y, et al. 1996. Cell 86:311-19
97. Ames BN. 1989. Free Radic. Res. Commun. 7:121-28
98. Hinrichsen LI, Floyd RA, Sudilovsky O. 1990. Carcinogenesis 11:1879-81
99. Ames BN, Shigenaga MK, Hagen TM. 1995. Biochim. Biophys. Acta 1271:165-70
100. Richter C. 1995. Int. J. Biochem. Cell Biol. 27:647-53
101. Grollman AP, Moriya M. 1993. Trends Genet. 9:246-49
102. Tchou J, Grollman AP. 1993. Mutat. Res. 299:277-87
103. Harwood J, Tachibana A, Meuth M. 1991. Mol. Cell. Biol. 11:3163-70
104. Kitamura Y, Goodfellow PJ, Shimizu K, Nagahama M, Ito K, et al. 1997. Oncogene 14:3103-6
105. Michaels ML, Miller, JH. 1992. J. Bacteriol. 174:6321-25
106. Tajiri T, Maki H, Sekiguchi M. 1995. Mutat. Res. 336:257-67
107. Shibutani S, Takeshita M, Grollman AP. 1991. Nature 349:431-34
108. Kouchakdjian M, Eisenberg M, Johnson F, Grollman AP, Patel DJ. 1991. Biochemistry 30:3262-70
109. Tchou J, Kasai H, Shibutani S, Chung MH, Laval J, et al. 1991. Proc. Natl. Acad. Sci. USA 88:4690-94
110. Michaels ML, Cruz C, Grollman AP, Miller JH. 1992. Proc. Natl. Acad. Sci. USA 89:7022-25
111. Michaels ML, Pham L, Nghiem Y, Cruz C, Miller JH. 1990. Nucleic Acids Res. 18:3841-45
112. Lu AL, Tsai-Wu JJ, Cillo J. 1995. J. Biol. Chem. 270:23582-88
113. Manuel RC, Lloyd RS. 1997. Biochemistry 36:11140-52
114. McGoldrick JP, Yeh YC, Solomon M, Essigmann JM, Lu AL. 1995. Mol. Cell. Biol. 15:989-96
115. Slupska MM, Baikalov C, Luther WM, Chiang JH, Wei YF, Miller JH. 1996. J. Bacteriol. 178:3885-92
116. Manuel RC, Czerwinski EW, Lloyd RS. 1996. J. Biol. Chem. 271:16218-26
117. Guan Y, Manuel RC, Arvai AS, Parikh SS, Mol CD, et al. 1998. Nature Struct. Biol. 5:22-27
118. O'Connor TR, Graves RJ, de Murcia G, Castaing B, Laval J. 1993. J. Biol. Chem. 268:9063-70
119. Bhagwat M, Gerlt JA. 1996. Biochemistry 35:659-45
120. Tchou J, Bodepudi V, Shibutani S, Antoshechkin I, Miller J, et al. 1994. J. Biol. Chem. 269:15318-24
121. Croteau DL, Bohr VA. 1997. J. Biol. Chem. 272:25409-12
122. Boiteux S. 1993. J. Photochem. Photobiol. 19:87-96
123. Duwat P, de Oliveira R, Ehrlich SD, Boiteux S. 1995. Microbiology 141:411-17
124. de Oliveira R, van der Kemp PA, Thomas D, Geiger A, Nehls P, Boiteux S. 1994. Nucleic Acids Res. 22:3760-64
125. Bessho T, Tano K, Kasai H, Ohtsuka E, Nishimura S. 1993. J. Biol. Chem. 268:19416-21
126. Margison GP, Pegg AE. 1981. Proc. Natl. Acad. Sci. USA 78:861-65
127. van der Kemp PA, Thomas D, Barbey R, de Oliveira R, Boiteux S. 1996. Proc. Natl. Acad. Sci. USA 93:5197-202
128. Nash HM, Bruner SD, Schärer OD, Kawate T, Addona TA, et al. 1996. Curr: Biol. 6:968-80
129. Bruner SD, Nash HM, Lane WS, Verdine GL. 1998. Curr. Biol. 8:393-403
130. Aburatani H, Hippo Y, Ishida T, Takashima R, Matsuba C, et al. 1997. Cancer Res. 57:2151-56
131. Bjoras M, Luna L, Johnsen B, Hoff E, Haug T, et al. 1997. EMBO J. 16:6314-22
132. Shinmura K, Kasai H, Sasaki A, Sugimura H, Yokota J. 1997. Mutat. Res. 385:75-82
133. Lu R, Nash HM, Verdine GL. 1997. Curr. Biol. 7:397-407
134. Rosenquist TA, Zharkov DO, Grollman AP. 1997. Proc. Natl. Acad. Sci. USA 94:7429-34
135. Yacoub A, Augeri L, Kelley MR, Doetsch PW, Deutsch WA. 1996. EMBO J. 15:2306-12
136. Deutsch WA, Yacoub A, Jaruga P, Zastawny TH, Dizdaroglu M. 1997. J. Biol. Chem. 272:32857-60
137. Zharkov DO, Rieger RA, Iden CR, Grollman AP. 1997. J. Biol. Chem. 272:5335-41
138. Tchou J, Grollman AP. 1995. J. Biol. Chem. 270:11671-77
139. Nash HM, Lu R, Lane WS, Verdine GL. 1997. Chem. Biol. 4:693-702
140. Kow YW, Wallace SS. 1987. Biochemistry 26:8200-6
141. Gruskin EA, Lloyd RS. 1988. J. Biol. Chem. 263:12728-37
142. Sandigursky M, Franklin WA. 1992. Nucleic Acids Res. 20:4699-703
143. Dianov G, Lindahl T. 1994. Curr. Biol. 4:1069-76
144. Matsumoto Y, Kim K, Bogenhagen DF. 1994. Mol. Cell. Biol. 14:6187-97
145. Frosina G, Fortini P, Rossi O, Carrozzino F, Raspaglio G, et al. 1996. J. Biol. Chem. 271:9573-78
146. Fortini P, Pascucci B, Parlanti E, Sobol RW, Wilson SH, Dogliotti E. 1998. Biochemistry 37:3575-80
147. Sandigursky M, Freyer GA, Franklin WA. 1998. Nucleic Acids Res. 26:1282-87
148. Savio M, Stivala LA, Bianchi L, Vannini V, Prosperi E. 1998. Carcinogenesis 19:591-96
149. Dianov G, Price A, Lindahl T. 1992. Mol. Cell. Biol. 12:1605-12
150. Singhal RK, Prasad R, Wilson SH. 1995. J. Biol. Chem. 270:949-57
151. Kubota Y, Nash RA, Klungland A, Schar P, Barnes DE, Lindahl T. 1996. EMBO J. 15:6662-70
152. Nicholl ID, Nealon K, Kenny MK. 1997. Biochemistry 36:7557-66
153. Wang Z, Wu X, Friedberg EC. 1997. J. Biol. Chem. 272:24064-71
154. Klungland A, Lindahl T. 1997. EMBO J. 16:3341-48
155. Biade S, Sobol RW, Wilson SH, Matsumoto Y. 1998. J. Biol. Chem. 273:898-902
156. Kim K, Biade S, Matsumoto Y. 1998. J. Biol. Chem. 273:8842-48
157. Matsumoto Y, Kim K. 1995. Science 269:699-702
158. Piersen CE, Prasad R, Wilson SH, Lloyd RS. 1996. J. Biol. Chem. 271:17811-15
159. Prasad R, Singhal RK, Srivastava DK, Molina JT, Tomkinson AE, Wilson SH. 1996. J. Biol. Chem. 271:16000-7
160. Dimitriadis EK, Prasad R, Vaske MK, Chen L, Tomkinson AE, et al. 1998. J. Biol. Chem. 273:20540-50
161. Bennett RA, Wilson DM, Wong D, Demple B. 1997. Proc. Natl. Acad. Sci. USA 94:7166-69
162. Sandigursky M, Mendez F, Bases RE. Matsumoto T, Franklin WA. 1996. Radiat. Res. 145:619-23
163. Cappelli E, Taylor R, Cevasco M, Abbondandolo A, Caldecott K, Frosina G. 1997. J. Biol. Chem. 272:23970-75
164. Masson M, Niedergang C, Schreiber V, Muller S, Menissier-de Murcia J, de Murcia G. 1998. Mol. Cell. Biol. 18:3563-71
165. Zdzienicka MZ, van der Schans GP, Natarajan AT, Thompson LH, Neuteboom I, Simons JW. 1992. Mutagenesis 7:265-69
166. Trucco C, Oliver FJ, de Murcia G, Menissier-de Murcia J. 1998. Nucleic Acids Res. 26:2644-49
167. Muller-Weeks SJ, Caradonna S. 1996. Exp. Cell. Res. 226:346-55
168. Scicchitano DA, Mellon I. 1997. Environ. Health Perspect. 105:(Suppl. 1) 145-53
169. Vrieling H, van Zeeland AA, Mullenders LHF. 1998. Mutat. Res. 400:135-42
170. Cooper PK, Nouspikel T, Clarkson SG, Leadon SA. 1997. Science 275:990-93
171. Leadon SA, Avrutskaya AV. 1998. Mutat. Res. 407:177-87
172. Gowen LC, Avrutskaya AV, Latour AM, Koller BH, Leadon SA. 1998. Science 281:1009-12
173. Kraulis P. 1991. J. Appl. Crystall. 24:946-50