Identification of catalytic metal ion ligands in ribozymes

Methods

Volumn 49, Issue 2, 2009, Pages 148-166

  Frederiksen, John K ^a   Piccirilli, Joseph A ^b  

^a UNIVERSITY OF CHICAGO   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

Author keywords

Catalysis; EPR; Isotope effects; Metal ion rescue; Metal ion ligand interactions; NMR; Ribozymes; RNA; RNase P; Tetrahymena group I ribozyme; X ray crystallography

Indexed keywords

COBALT; EUROPIUM; GUANOSINE; IRIDIUM; ISOTOPE; LEAD; LIGAND; MANGANESE; METAL ION; OXYGEN; PHOSPHATE; RIBONUCLEASE P; RIBOZYME; TERBIUM;

BINDING AFFINITY; BINDING SITE; CATALYSIS; CRYSTAL STRUCTURE; HEPATITIS DELTA VIRUS; INTRON; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; REVIEW; RNA STRUCTURE; TETRAHYMENA; X RAY CRYSTALLOGRAPHY;

BIOPHYSICS; CATALYSIS; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; IONS; LIGANDS; METALS; MODELS, CHEMICAL; MOLECULAR CONFORMATION; RIBONUCLEASE P; RNA, CATALYTIC; SOFTWARE; SPECTROPHOTOMETRY; STATIC ELECTRICITY; TETRAHYMENA;

TETRAHYMENA;

EID: 70349279881     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2009.07.005     Document Type: Review

References (188)

1. Herschlag D., and Cech T.R. Biochemistry 29 (1990) 10159-10171
2. Pyle A.M. Science 261 (1993) 709-714
3. Murray J.B., Seyhan A.A., Walter N.G., Burke J.M., and Scott W.G. Chem. Biol. 5 (1998) 587-595
4. Nakano S., Chadalavada D.M., and Bevilacqua P.C. Science 287 (2000) 1493-1497
5. Perrotta A.T., and Been M.D. Biochemistry 45 (2006) 11357-11365
6. Roth A., Nahvi A., Lee M., Jona I., and Breaker R.R. RNA 12 (2006) 607-619
7. Sigel R.K., and Pyle A.M. Chem. Rev. 107 (2007) 97-113
8. Bukhman Y.V., and Draper D.E. J. Mol. Biol. 273 (1997) 1020-1031
9. Nakano S., Proctor D.J., and Bevilacqua P.C. Biochemistry 40 (2001) 12022-12038
10. Nakano S., Cerrone A.L., and Bevilacqua P.C. Biochemistry 42 (2003) 2982-2994
11. Nakano S., and Bevilacqua P.C. Biochemistry 46 (2007) 3001-3012
12. Ke A., Zhou K., Ding F., Cate J.H., and Doudna J.A. Nature 429 (2004) 201-205
13. Chen J.H., Gong B., Bevilacqua P.C., Carey P.R., and Golden B.L. Biochemistry 48 (2009) 1498-1507
14. Williams L.D. Top. Curr. Chem. 253 (2005) 77-88
15. Adams P.L., Stahley M.R., Kosek A.B., Wang J., and Strobel S.A. Nature 430 (2004) 45-50
16. Guo F., Gooding A.R., and Cech T.R. Mol. Cell 16 (2004) 351-362
17. Golden B.L., Kim H., and Chase E. Nat. Struct. Mol. Biol. 12 (2005) 82-89
18. Stahley M.R., and Strobel S.A. Science 309 (2005) 1587-1590
19. Toor N., Keating K.S., Taylor S.D., and Pyle A.M. Science 320 (2008) 77-82
20. Toor N., Rajashankar K., Keating K.S., and Pyle A.M. Nat. Struct. Mol. Biol. 15 (2008) 1221-1222
21. Krasilnikov A.S., Yang X., Pan T., and Mondragon A. Nature 421 (2003) 760-764
22. Kazantsev A.V., Krivenko A.A., Harrington D.J., Holbrook S.R., Adams P.D., and Pace N.R. Proc. Natl. Acad. Sci. USA 102 (2005) 13392-13397
23. Torres-Larios A., Swinger K.K., Krasilnikov A.S., Pan T., and Mondragon A. Nature 437 (2005) 584-587
24. Ban N., Nissen P., Hansen J., Moore P.B., and Steitz T.A. Science 289 (2000) 905-920
25. Wimberly B.T., Brodersen D.E., Clemons Jr. W.M., Morgan-Warren R.J., Carter A.P., Vonrhein C., Hartsch T., and Ramakrishnan V. Nature 407 (2000) 327-339
26. Clemons Jr. W.M., Brodersen D.E., McCutcheon J.P., May J.L., Carter A.P., Morgan-Warren R.J., Wimberly B.T., and Ramakrishnan V. J. Mol. Biol. 310 (2001) 827-843
27. Pley H.W., Lindes D.S., DeLuca-Flaherty C., and McKay D.B. J. Biol. Chem. 268 (1993) 19656-19658
28. Pley H.W., Flaherty K.M., and McKay D.B. Nature 372 (1994) 68-74
29. Scott W.G., Finch J.T., and Klug A. Nucleic Acids Symp. Ser. (1995) 214-216
30. Scott W.G., Murray J.B., Arnold J.R., Stoddard B.L., and Klug A. Science 274 (1996) 2065-2069
31. Martick M., and Scott W.G. Cell 126 (2006) 309-320
32. Rupert P.B., and Ferre-D'Amare A.R. Nature 410 (2001) 780-786
33. Rupert P.B., Massey A.P., Sigurdsson S.T., and Ferre-D'Amare A.R. Science 298 (2002) 1421-1424
34. Ferre-D'Amare A.R., Zhou K., and Doudna J.A. Nature 395 (1998) 567-574
35. Ferre-D'Amare A.R., and Doudna J.A. J. Mol. Biol. 295 (2000) 541-556
36. Klein D.J., and Ferre-D'Amare A.R. Science 313 (2006) 1752-1756
37. Ye J.D., Tereshko V., Frederiksen J.K., Koide A., Fellouse F.A., Sidhu S.S., Koide S., Kossiakoff A.A., and Piccirilli J.A. Proc. Natl. Acad. Sci. USA 105 (2008) 82-87
38. Kovall R.A., and Matthews B.W. Curr. Opin. Chem. Biol. 3 (1999) 578-583
39. Pingoud A., and Jeltsch A. Nucleic Acids Res. 29 (2001) 3705-3727
40. Galburt E.A., and Stoddard B.L. Biochemistry 41 (2002) 13851-13860
41. Nelson J.A., and Uhlenbeck O.C. Mol. Cell 23 (2006) 447-450
42. DeRose V.J. In: Hud N.V. (Ed). Nucleic Acid-Metal Ion Interactions (2009), Royal Society of Chemistry, Cambridge, UK 154-179
43. Horton T.E., Clardy D.R., and DeRose V.J. Biochemistry 37 (1998) 18094-18101
44. Morrissey S.R., Horton T.E., and DeRose V.J. J. Am. Chem. Soc. 122 (2000) 3473-3481
45. Kisseleva N., Khvorova A., Westhof E., and Schiemann O. RNA 11 (2005) 1-6
46. Vogt M., Lahiri S., Hoogstraten C.G., Britt R.D., and DeRose V.J. J. Am. Chem. Soc. 128 (2006) 16764-16770
47. Salemink P.J., Swarthof T., and Hilbers C.W. Biochemistry 18 (1979) 3477-3485
48. Hilbers C.W., Heerschap A., Haasnoot C.A., and Walters J.A. J. Biomol. Struct. Dyn. 1 (1983) 183-207
49. Cheong C., Varani G., and Tinoco Jr. I. Nature 346 (1990) 680-682
50. Dieckmann T., Suzuki E., Nakamura G.K., and Feigon J. RNA 2 (1996) 628-640
51. Butcher S.E., Dieckmann T., and Feigon J. EMBO J. 16 (1997) 7490-7499
52. Sashital D.G., Venditti V., Angers C.G., Cornilescu G., and Butcher S.E. RNA 13 (2007) 328-338
53. Wu M., and Tinoco Jr. I. Proc. Natl. Acad. Sci. USA 95 (1998) 11555-11560
54. Al-Hashimi H.M., Pitt S.W., Majumdar A., Xu W., and Patel D.J. J. Mol. Biol. 329 (2003) 867-873
55. Maderia M., Hunsicker L.M., and DeRose V.J. Biochemistry 39 (2000) 12113-12120
56. Butcher S.E., Allain F.H., and Feigon J. Biochemistry 39 (2000) 2174-2182
57. Noeske J., Schwalbe H., and Wohnert J. Nucleic Acids Res. 35 (2007) 5262-5273
58. Reid S.S., and Cowan J.A. Biochemistry 29 (1990) 6025-6032
59. Grant C.V., Frydman V., and Frydman L. J. Am. Chem. Soc. 122 (2000) 11743-11744
60. Grant C.V., Frydman V., Harwood J.S., and Frydman L. J. Am. Chem. Soc. 124 (2002) 4458-4462
61. Marincola F.C., Casu M., Saba G., Manetti C., and Lai A. Phys. Chem. Chem. Phys. 2 (2000) 2425-2428
62. Denisov V.P., and Halle B. Proc. Natl. Acad. Sci. USA 97 (2000) 629-633
63. Marincola F.C., Denisov V.P., and Halle B. J. Am. Chem. Soc. 126 (2004) 6739-6750
64. Gill M.L., Strobel S.A., and Loria J.P. J. Am. Chem. Soc. 127 (2005) 16723-16732
65. L.M. Hunsicker-Wang, Ph.D. Thesis, Texas A&M University, 2001.
66. Kayne M.S., and Cohn M. Biochemistry 13 (1974) 4159-4165
67. Draper D.E. Biophys Chem 21 (1985) 91-101
68. Greenbaum N.L., Mundoma C., and Peterman D.R. Biochemistry 40 (2001) 1124-1134
69. Yuan F., Griffin L., Phelps L., Buschmann V., Weston K., and Greenbaum N.L. Nucleic Acids Res. 35 (2007) 2833-2845
70. Feig A.L., Panek M., Horrocks Jr. W.D., and Uhlenbeck O.C. Chem. Biol. 6 (1999) 801-810
71. Walter N.G., Yang N., and Burke J.M. J. Mol. Biol. 298 (2000) 539-555
72. Tinsley R.A., and Walter N.G. Biol. Chem. 388 (2007) 705-715
73. Gong B., Chen Y., Christian E.L., Chen J.H., Chase E., Chadalavada D.M., Yajima R., Golden B.L., Bevilacqua P.C., and Carey P.R. J. Am. Chem. Soc. 130 (2008) 9670-9672
74. Chin K., Sharp K.A., Honig B., and Pyle A.M. Nat. Struct. Biol. 6 (1999) 1055-1061
75. Hermann T., and Westhof E. Structure 6 (1998) 1303-1314
76. Bagley S.C., and Altman R.B. Protein Sci. 4 (1995) 622-635
77. Banatao D.R., Altman R.B., and Klein T.E. Nucleic Acids Res. 31 (2003) 4450-4460
78. Castagnetto J.M., Hennessy S.W., Roberts V.A., Getzoff E.D., Tainer J.A., and Pique M.E. Nucleic Acids Res. 30 (2002) 379-382
79. Stefan L.R., Zhang R., Levitan A.G., Hendrix D.K., Brenner S.E., and Holbrook S.R. Nucleic Acids Res. 34 (2006) D131-D134
80. Klosterman P.S., Tamura M., Holbrook S.R., and Brenner S.E. Nucleic Acids Res. 30 (2002) 392-394
81. Sigel R.K., Vaidya A., and Pyle A.M. Nat. Struct. Biol. 7 (2000) 1111-1116
82. Kaye N.M., Zahler N.H., Christian E.L., and Harris M.E. J. Mol. Biol. 324 (2002) 429-442
83. Harris D.A., Tinsley R.A., and Walter N.G. J. Mol. Biol. 341 (2004) 389-403
84. Hargittai M.R., and Musier-Forsyth K. RNA 6 (2000) 1672-1680
85. Harris D.A., and Walter N.G. Curr. Protoc. Nucleic Acid Chem. Chap. 6 (2003) Unit 6.8
86. Harris M.E., and Cassano A.G. Curr. Opin. Chem. Biol. 12 (2008) 626-639
87. Buddenbaum W.E., and Shiner V.J. Can. J. Chem. 54 (1976) 1146-1161
88. Paneth P., and Oleary M.H. J. Am. Chem. Soc. 113 (1991) 1691-1693
89. Hengge A.C., Sowa G.A., Wu L., and Zhang Z.Y. Biochemistry 34 (1995) 13982-13987
90. Hengge A.C., Bruzik K.S., Tobin A.E., Cleland W.W., and Tsai M.D. Bioorg. Chem. 28 (2000) 119-133
91. Gerratana B., Sowa G.A., and Cleland W.W. J. Am. Chem. Soc. 122 (2000) 12615-12621
92. Cassano A.G., Anderson V.E., and Harris M.E. J. Am. Chem. Soc. 124 (2002) 10964-10965
93. Shih I.H., and Been M.D. Proc. Natl. Acad. Sci. USA 98 (2001) 1489-1494
94. Smith M.D., and Collins R.A. Proc. Natl. Acad. Sci. USA 104 (2007) 5818-5823
95. Rishavy M.A., Hengge A.C., and Cleland W.W. Bioorg. Chem. 28 (2000) 283-292
96. Humphry T., Forconi M., Williams N.H., and Hengge A.C. J. Am. Chem. Soc. 124 (2002) 14860-14861
97. Rawlings J., Cleland W.W., and Hengge A.C. J. Inorg. Biochem. 93 (2003) 61-65
98. Humphry T., Forconi M., Williams N.H., and Hengge A.C. J. Am. Chem. Soc. 126 (2004) 11864-11869
99. Yang M.Y., Iranzo O., Richard J.P., and Morrow J.R. J. Am. Chem. Soc. 127 (2005) 1064-1065
100. Rawlings J., Cleland W.W., and Hengge A.C. J. Am. Chem. Soc. 128 (2006) 17120-17125
101. Cassano A.G., Anderson V.E., and Harris M.E. Biochemistry 43 (2004) 10547-10559
102. Cassano A.G., Anderson V.E., and Harris M.E. Biopolymers 73 (2004) 110-129
103. Dai Q., Frederiksen J.K., Anderson V.E., Harris M.E., and Piccirilli J.A. J. Org. Chem. 73 (2008) 309-311
104. Zhong M., and Strobel S.A. J. Org. Chem. 73 (2008) 603-611
105. Ryder S.P., and Strobel S.A. Methods 18 (1999) 38-50
106. Freisinger E., and Sigel R.K.O. Coord. Chem. Rev. 251 (2007) 1834-1851
107. Klein D.J., Moore P.B., and Steitz T.A. RNA 10 (2004) 1366-1379
108. Christian E.L., and Yarus M. Biochemistry 32 (1993) 4475-4480
109. Szewczak A.A., Kosek A.B., Piccirilli J.A., and Strobel S.A. Biochemistry 41 (2002) 2516-2525
110. Hougland J.L., Kravchuk A.V., Herschlag D., and Piccirilli J.A. PLoS Biol. 3 (2005) e277
111. Forconi M., Lee J., Lee J.K., Piccirilli J.A., and Herschlag D. Biochemistry 47 (2008) 6883-6894
112. Sarnovsky R.J., May E.W., and Craig N.L. Embo J. 15 (1996) 6348-6361
113. Allingham J.S., Pribil P.A., and Haniford D.B. J. Mol. Biol. 289 (1999) 1195-1206
114. Kim D.R., Dai Y., Mundy C.L., Yang W., and Oettinger M.A. Genes Dev. 13 (1999) 3070-3080
115. Landree M.A., Wibbenmeyer J.A., and Roth D.B. Genes Dev. 13 (1999) 3059-3069
116. Gao K., Wong S., and Bushman F. J. Virol. 78 (2004) 6715-6722
117. Schwarzer D., and Cole P.A. Curr. Opin. Chem. Biol. 9 (2005) 561-569
118. Piccirilli J.A., Vyle J.S., Caruthers M.H., and Cech T.R. Nature 361 (1993) 85-88
119. Sjögren A.S., Pettersson E., Sjöberg B.M., and Strömberg R. Nucleic Acids Res. 25 (1997) 648-653
120. Weinstein L.B., Jones B.C., Cosstick R., and Cech T.R. Nature 388 (1997) 805-808
121. Shan S., Yoshida A., Sun S., Piccirilli J.A., and Herschlag D. Proc. Natl. Acad. Sci. USA 96 (1999) 12299-12304
122. Shan S.O., and Herschlag D. Biochemistry 38 (1999) 10958-10975
123. Yoshida A., Sun S., and Piccirilli J.A. Nat. Struct. Biol. 6 (1999) 318-321
124. Shan S., Kravchuk A.V., Piccirilli J.A., and Herschlag D. Biochemistry 40 (2001) 5161-5171
125. Sontheimer E.J., Gordon P.M., and Piccirilli J.A. Genes Dev. 13 (1999) 1729-1741
126. Gordon P.M., Sontheimer E.J., and Piccirilli J.A. Biochemistry 39 (2000) 12939-12952
127. Gordon P.M., and Piccirilli J.A. Nat. Struct. Biol. 8 (2001) 893-898
128. Gordon P.M., Fong R., and Piccirilli J.A. Chem. Biol. 14 (2007) 607-612
129. Peracchi A., Beigelman L., Scott E.C., Uhlenbeck O.C., and Herschlag D. J. Biol. Chem. 272 (1997) 26822-26826
130. Wang S., Karbstein K., Peracchi A., Beigelman L., and Herschlag D. Biochemistry 38 (1999) 14363-14378
131. Osborne E.M., Schaak J.E., and DeRose V.J. RNA 11 (2005) 187-196
132. Warnecke J.M., Furste J.P., Hardt W.D., Erdmann V.A., and Hartmann R.K. Proc. Natl. Acad. Sci. USA 93 (1996) 8924-8928
133. Chen Y., Li X., and Gegenheimer P. Biochemistry 36 (1997) 2425-2438
134. Warnecke J.M., Held R., Busch S., and Hartmann R.K. J. Mol. Biol. 290 (1999) 433-445
135. Pfeiffer T., Tekos A., Warnecke J.M., Drainas D., Engelke D.R., Seraphin B., and Hartmann R.K. J. Mol. Biol. 298 (2000) 559-565
136. Christian E.L., Kaye N.M., and Harris M.E. RNA 6 (2000) 511-519
137. Christian E.L., Kaye N.M., and Harris M.E. Embo J. 21 (2002) 2253-2262
138. Persson T., Cuzic S., and Hartmann R.K. J. Biol. Chem. 278 (2003) 43394-43401
139. Christian E.L., Smith K.M., Perera N., and Harris M.E. RNA 12 (2006) 1463-1467
140. Sontheimer E.J., Sun S., and Piccirilli J.A. Nature 388 (1997) 801-805
141. Gordon P.M., Sontheimer E.J., and Piccirilli J.A. RNA 6 (2000) 199-205
142. Yean S.L., Wuenschell G., Termini J., and Lin R.J. Nature 408 (2000) 881-884
143. Pecoraro V.L., Hermes J.D., and Cleland W.W. Biochemistry 23 (1984) 5262-5271
144. Frey P.A., and Sammons R.D. Science 228 (1985) 541-545
145. Rablen P.R., Lockman J.W., and Jorgensen W.L. J. Phys. Chem. A 102 (1998) 3782-3797
146. Brautigam C.A., and Steitz T.A. J. Mol. Biol. 277 (1998) 363-377
147. Kruger K., Grabowski P.J., Zaug A.J., Sands J., Gottschling D.E., and Cech T.R. Cell 31 (1982) 147-157
148. Zaug A.J., Been M.D., and Cech T.R. Nature 324 (1986) 429-433
149. Grosshans C.A., and Cech T.R. Biochemistry 28 (1989) 6888-6894
150. Bevilacqua P.C., Kierzek R., Johnson K.A., and Turner D.H. Science 258 (1992) 1355-1358
151. Herschlag D. Biochemistry 31 (1992) 1386-1399
152. Herschlag D., and Khosla M. Biochemistry 33 (1994) 5291-5297
153. Cosstick R., and Vyle J.S. Nucleic Acids Res. 18 (1990) 829-835
154. Vyle J.S., Connolly B.A., Kemp D., and Cosstick R. Biochemistry 31 (1992) 3012-3018
155. Herschlag D., and Cech T.R. Nature 344 (1990) 405-409
156. Shan S.O., and Herschlag D. RNA 6 (2000) 795-813
157. Steitz T.A., and Steitz J.A. Proc. Natl. Acad. Sci. USA 90 (1993) 6498-6502
158. Freemont P.S., Friedman J.M., Beese L.S., Sanderson M.R., and Steitz T.A. Proc. Natl. Acad. Sci. USA 85 (1988) 8924-8928
159. Beese L.S., and Steitz T.A. Embo J. 10 (1991) 25-33
160. Kim E.E., and Wyckoff H.W. J. Mol. Biol. 218 (1991) 449-464
161. Dantzman C.L., and Kiessling L.L. J. Am. Chem. Soc. 118 (1996) 11715-11719
162. Bass B.L., and Cech T.R. Nature 308 (1984) 820-826
163. McConnell T.S., and Cech T.R. Biochemistry 34 (1995) 4056-4067
164. Gott J.M., Shub D.A., and Belfort M. Cell 47 (1986) 81-87
165. Stromberg R., Hahne S., Sjogren A.S., and Sjoberg B.M. Biochem. Biophys. Res. Commun. 183 (1992) 842-848
166. Shan S.O., and Herschlag D. RNA 8 (2002) 861-872
167. Herschlag D., Piccirilli J.A., and Cech T.R. Biochemistry 30 (1991) 4844-4854
168. Michel F., and Westhof E. J. Mol. Biol. 216 (1990) 585-610
169. Ortoleva-Donnelly L., Szewczak A.A., Gutell R.R., and Strobel S.A. RNA 4 (1998) 498-519
170. Strauss-Soukup J.K., and Strobel S.A. J. Mol. Biol. 302 (2000) 339-358
171. Moore M.J., and Sharp P.A. Science 256 (1992) 992-997
172. M. Forconi, J. Lee, J.L. Hougland, J.A. Piccirilli, D. Herschlag, unpublished.
173. Guo F., and Cech T.R. Nat. Struct. Biol. 9 (2002) 855-861
174. Evans D., Marquez S.M., and Pace N.R. Trends Biochem. Sci. 31 (2006) 333-341
175. Kazantsev A.V., and Pace N.R. Nat. Rev. Microbiol. 4 (2006) 729-740
176. Wang M.J., Davis N.W., and Gegenheimer P. Embo J. 7 (1988) 1567-1574
177. Guerrier-Takada C., Gardiner K., Marsh T., Pace N., and Altman S. Cell 35 (1983) 849-857
178. Pannucci J.A., Haas E.S., Hall T.A., Harris J.K., and Brown J.W. Proc. Natl. Acad. Sci. USA 96 (1999) 7803-7808
179. Beebe J.A., Kurz J.C., and Fierke C.A. Biochemistry 35 (1996) 10493-10505
180. Smith D., and Pace N.R. Biochemistry 32 (1993) 5273-5281
181. Kahle D., Kust B., and Krupp G. Biochimie 75 (1993) 955-962
182. Warnecke J.M., Green C.J., and Hartmann R.K. Nucleosides Nucleotides 16 (1997) 721-725
183. Warnecke J.M., Sontheimer E.J., Piccirilli J.A., and Hartmann R.K. Nucleic Acids Res. 28 (2000) 720-727
184. Loria A., and Pan T. Biochemistry 37 (1998) 10126-10133
185. Chen J.L., and Pace N.R. RNA 3 (1997) 557-560
186. Harris M.E., and Pace N.R. RNA 1 (1995) 210-218
187. Kaye N.M., Christian E.L., and Harris M.E. Biochemistry 41 (2002) 4533-4545
188. Crary S.M., Kurz J.C., and Fierke C.A. RNA 8 (2002) 933-947