The structure and function of catalytic RNAs

Science in China, Series C: Life Sciences

Volumn 52, Issue 3, 2009, Pages 232-244

  Wu, QiJia ^a   Huang, Lin ^a   Zhang, Yi ^a  

^a WUHAN UNIVERSITY   (China)

Author keywords

Catalysis; Ribozyme; Structure

Indexed keywords

RIBONUCLEASE P; RIBOZYME; RNA;

BINDING SITE; CATALYSIS; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; ENZYME SPECIFICITY; FORECASTING; GENETICS; INTRON; METABOLISM; PROTEIN BINDING; PROTEIN TERTIARY STRUCTURE; REVIEW; STRUCTURE ACTIVITY RELATION;

BINDING SITES; CATALYSIS; FORECASTING; INTRONS; MODELS, CHEMICAL; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; RIBONUCLEASE P; RNA; RNA, CATALYTIC; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY;

TETRAHYMENA;

EID: 63049102737     PISSN: 10069305     EISSN: 18622798     Source Type: Journal    
DOI: 10.1007/s11427-009-0038-z     Document Type: Review

References (76)

1. K. Kruger P. J. Grabowski A. J. Zaug 1982 Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena Cell 31 1 147 157
2. C. Guerrier-Takada K. Gardiner T. Marsh 1983 The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme Cell 35 3Pt2 849 857
3. S. E. Butcher 2001 Structure and function of the small ribozymes Curr Opin Struct Biol 11 3 315 320
4. Y. Zhou C. Lu Q. J. Wu 2008 GISSD: Group I intron sequence and structure database Nucleic Acids Res 36 D31 37
5. O. Fedorova N. Zingler 2007 Group II introns: structure, folding and splicing mechanism Biol Chem 388 7 665 678
6. P. Haugen D. M. Simon D. Bhattacharya 2005 The natural history of group I introns Trends Genet 21 2 111 119
7. A. V. Kazantsev N. R. Pace 2006 Bacterial RNase P: a new view of an ancient enzyme Nat Rev Microbiol 4 10 729 740
8. T. R. Cech 2000 Structural biology. The ribosome is a ribozyme Science 289 5481 878 879
9. H. W. Pley K. M. Flaherty D. B. McKay 1994 Three-dimensional structure of a hammerhead ribozyme Nature 372 6501 68 74
10. D. M. Lilley 2003 The origins of RNA catalysis in ribozymes Trends Biochem Sci 28 9 495 501
11. D. M. Lilley 2005 Structure, folding and mechanisms of ribozymes Curr Opin Struct Biol 15 3 313 323
12. S. Nakano D. M. Chadalavada P. C. Bevilacqua 2000 General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme Science 287 5457 1493 1497
13. D. B. McKay 1996 Structure and function of the hammerhead ribozyme: an unfinished story RNA 2 5 395 403
14. M. Martick W. G. Scott 2006 Tertiary contacts distant from the active site prime a ribozyme for catalysis Cell 126 2 309 320
15. J. A. Nelson O. C. Uhlenbeck 2006 When to believe what you see Mol Cell 23 4 447 450
16. N. G. Walter J. M. Burke 1998 The hairpin ribozyme: structure, assembly and catalysis Curr Opin Chem Biol 2 1 24 30
17. P. B. Rupert A. R. Ferre-D'Amare 2001 Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis Nature 410 6830 780 786
18. D. A. Lafontaine D. G. Norman D. M. Lilley 2001 Structure, folding and activity of the VS ribozyme: importance of the 2-3-6 helical junction EMBO J 20 6 1415 1424
19. A. A. Andersen R. A. Collins 2000 Rearrangement of a stable RNA secondary structure during VS ribozyme catalysis Mol Cell 5 3 469 478
20. S. L. Hiley V. D. Sood J. Fan 2002 4-thio-U cross-linking identifies the active site of the VS ribozyme Embo J 21 17 4691 4698
21. B. Hoffmann G. T. Mitchell P. Gendron 2003 NMR structure of the active conformation of the Varkud satellite ribozyme cleavage site Proc Natl Acad Sci USA 100 12 7003 7008
22. A. T. Perrotta M. D. Been 1991 A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta virus RNA Nature 350 6317 434 436
23. A. R. Ferre-D'Amare K. Zhou J. A. Doudna 1998 Crystal structure of a hepatitis delta virus ribozyme Nature 395 6702 567 574
24. S. R. Das J. A. Piccirilli 2005 General acid catalysis by the hepatitis delta virus ribozyme Nat Chem Biol 1 1 45 52
25. A. Ke K. Zhou F. Ding 2004 A conformational switch controls hepatitis delta virus ribozyme catalysis Nature 429 6988 201 205
26. S. Xiao F. Scott C. A. Fierke 2002 Eukaryotic ribonuclease P: a plurality of ribonucleoprotein enzymes Annu Rev Biochem 71 165 189
27. M. E. Harris E. L. Christian 2003 Recent insights into the structure and function of the ribonucleoprotein enzyme ribonuclease P Curr Opin Struct Biol 13 3 325 333
28. A. V. Kazantsev A. A. Krivenko D. J. Harrington 2005 Crystal structure of a bacterial ribonuclease P RNA Proc Natl Acad Sci USA 102 38 13392 13397
29. A. Torres-Larios K. K. Swinger A. S. Krasilnikov 2005 Crystal structure of the RNA component of bacterial ribonuclease P Nature 437 7058 584 587
30. M. Brannvall E. Kikovska L. Kirsebom 2004 Cross talk between the +73/294 interaction and the cleavage site in RNase P RNA mediated cleavage Nucleic Acids Res 32 5418 5429
31. S. Busch L. Kirsebom H. Notbohm 2000 Differential role of the intermolecular base-pairs G292-C(75) and G293-C(74) in the reaction catalyzed by Escherichia coli RNase P RNA J Mol Biol 299 941 951
32. D. Evans S. M. Marquez N. R. Pace P. RNase 2006 interface of the RNA and protein worlds Trends Biochem Sci 31 6 333 341
33. T. R. Cech 1990 Self-splicing of group I introns Annu Rev Biochem 59 543 568
34. E. A. Doherty J. A. Doudna 2000 Ribozyme structures and mechanisms Annu Rev Biochem 69 597 615
35. W. G. Scott 2007 Ribozymes Curr Opin Struct Biol 17 3 280 286
36. S. Shan A. Yoshida S. Sun 1999 Three metal ions at the active site of the Tetrahymena group I ribozyme Proc Natl Acad Sci USA 96 12299 12304
37. S. Strobel L. Ortoleva-Donnelly 1999 A hydrogen-bonding triad stabilizes the chemical transition state of a group I ribozyme Chem Biol 6 153 165
38. F. Michel E. Westhof 1990 Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis J Mol Biol 216 3 585 610
39. P. L. Adams M. R. Stahley A. B. Kosek 2004 Crystal structure of a self-splicing group I intron with both exons Nature 430 6995 45 50
40. J. H. Cate A. R. Gooding E. Podell 1996 Crystal structure of a group I ribozyme domain: principles of RNA packing Science 273 5282 1678 1685
41. B. L. Golden A. R. Gooding E. R. Podell 1998 A preorganized active site in the crystal structure of the Tetrahymena ribozyme Science 282 5387 259 264
42. B. L. Golden H. Kim E. Chase 2005 Crystal structure of a phage Twort group I ribozyme-product complex Nat Struct Mol Biol 12 1 82 89
43. M. A. Engelhardt E. A. Doherty D. S. Knitt 2000 The P5abc peripheral element facilitates preorganization of the tetrahymena group I ribozyme for catalysis Biochemistry 39 10 2639 2651
44. T. H. Johnson P. Tijerina A. B. Chadee 2005 Structural specificity conferred by a group I RNA peripheral element Proc Natl Acad Sci USA 102 29 10176 10181
45. M. Xiao T. Li X. Yuan 2005 A peripheral element assembles the compact core structure essential for group I intron self-splicing Nucleic Acids Res 33 14 4602 4611
46. A. Pichler R. Schroeder 2002 Folding problems of the 5′ splice site containing the P1 stem of the group I thymidylate synthase intron: substrate binding inhibition in vitro and mis-splicing in vivo J Biol Chem 277 20 17987 17993
47. A. A. Szewczak L. Ortoleva-Donnelly S. P. Ryder 1998 A minor groove RNA triple helix within the catalytic core of a group I intron Nat Struct Biol 5 12 1037 1042
48. J. M. Burke J. S. Esherick W. R. Burfeind 1990 A 3′ splice site-binding sequence in the catalytic core of a group I intron Nature 344 6261 80 82
49. B. M. Chowrira A. Berzal-Herranz J. M. Burke 1995 Novel system for analysis of group I 3′ splice site reactions based on functional trans-interaction of the P1/P10 reaction helix with the ribozyme's catalytic core Nucleic Acids Res 23 5 849 855
50. F. Guo A. R. Gooding T. R. Cech 2004 Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site Mol Cell 16 3 351 362
51. O. Zhaxybayeva J. P. Gogarten 2003 Spliceosomal introns: new insights into their evolution Curr Biol 13 19 R764 766
52. E. A. Griffin Jr Z. Qin W. J. Michels Jr 1995 Group II intron ribozymes that cleave DNA and RNA linkages with similar efficiency, and lack contacts with substrate 2′-hydroxyl groups Chem Biol 2 11 761 770
53. P. Z. Qin A. M. Pyle 1998 The architectural organization and mechanistic function of group II intron structural elements Curr Opin Struct Biol 8 3 301 308
54. A. de Lencastre A. M. Pyle 2008 Three essential and conserved regions of the group II intron are proximal to the 5′-splice site RNA 14 1 11 24
55. H. Wank J. SanFilippo R. N. Singh 1999 A reverse transcriptase/maturase promotes splicing by binding at its own coding segment in a group II intron RNA Mol Cell 4 2 239 250
56. U. Schmidt M. Podar U. Stahl 1996 Mutations of the two-nucleotide bulge of D5 of a group II intron block splicing in vitro and in vivo: phenotypes and suppressor mutations RNA 2 11 1161 1172
57. N. Toor K. S. Keating S. D. Taylor 2008 Crystal structure of a self-spliced group II intron Science 320 5872 77 82
58. N. Toor A. R. Robart J. Christianson 2006 Self-splicing of a group IIC intron: 5′ exon recognition and alternative 5′ splicing events implicate the stem-loop motif of a transcriptional terminator Nucleic Acids Res 34 22 6461 6471
59. M. Costa F. Michel E. Westhof 2000 A three-dimensional perspective on exon binding by a group II self-splicing intron EMBO J 19 12
60. A. Jacquier N. Jacquesson-Breuleux 1991 Splice site selection and role of the lariat in a group II intron J Mol Biol 219 14
61. M. Boudvillain A. M. Pyle 1998 Defining functional groups, core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: a NAIM analysis EMBO J 17 23 7091 7104
62. M. Costa F. Michel 1995 Frequent use of the same tertiary motif by self-folding RNAs EMBO J 14 6 1276 1285
63. S. Hamill A. M. Pyle 2006 The receptor for branch-site docking within a group II intron active site Mol Cell 23 6 831 840
64. D. L. Abramovitz R. A. Friedman A. M. Pyle 1996 Catalytic role of 2′-hydroxyl groups within a group II intron active site Science 271 5254 1410 1413
65. B. B. Konforti D. L. Abramovitz C. M. Duarte 1998 Ribozyme catalysis from the major groove of group II intron domain 5 Mol Cell 1 3 433 441
66. N. Ban P. Nissen J. Hansen 2000 The complete atomic structure of the large ribosomal subunit at 2.4 Å, resolution Science 289 5481 905 920
67. P. Nissen J. Hansen N. Ban 2000 The structural basis of ribosome activity in peptide bond synthesis Science 289 5481 920 930
68. H. F. Noller 2005 RNA structure: reading the ribosome Science 309 5740 1508 1514
69. B. S. Schuwirth M. A. Borovinskaya C. W. Hau 2005 Structures of the bacterial ribosome at 3.5 Å resolution Science 310 5749 827 834
70. A. Korostelev S. Trakhanov M. Laurberg 2006 Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements Cell 126 6 1065 1077
71. M. Selmer C. M. Dunham F. V. Murphy 2006 Structure of the 70S ribosome complexed with mRNA and tRNA Science 313 5795 1935 1942
72. L. Dai S. Zimmerly 2003 ORF-less and reverse-transcriptase-encoding group II introns in archaebacteria, with a pattern of homing into related group II intron ORFs RNA 9 1 14 19
73. A. S. Lewin W. W. Hauswirth 2001 Ribozyme gene therapy: applications for molecular medicine Trends Mol Med 7 5 221 228
74. P. J. Welch S. Yei J. R. Barber 1998 Ribozyme gene therapy for hepatitis C virus infection Clin Diagn Virol 10 2-3 163 171
75. E. A. Duarte M. C. Leavitt O. Yamada 1997 Hairpin ribozyme gene therapy for AIDS Methods Mol Biol 74 459 468
76. T. Watanabe B. A. Sullenger 2000 Induction of wild-type p53 activity in human cancer cells by ribozymes that repair mutant p53 transcripts Proc Natl Acad Sci USA 97 8490 8494