Structural principles of RNA catalysis in a 2′-5′ lariat-forming ribozyme

Journal of the American Chemical Society

Volumn 135, Issue 11, 2013, Pages 4403-4411

  Carlomagno, Teresa ^a   Amata, Irene ^a   Codutti, Luca ^a   Falb, Melanie ^a   Fohrer, Jörg ^b   Masiewicz, Pawel ^a   Simon, Bernd ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYTIC MECHANISMS; MAGNESIUM IONS; MUTATIONAL ANALYSIS; PRE-MRNA SPLICING; REACTION CENTER; SEQUENCE SPECIFICITY; SMALL ANGLE X-RAY SCATTERING; STRUCTURAL INSIGHTS;

ACTIVATION ANALYSIS; BIOMOLECULES; METAL IONS; QUANTUM CHEMISTRY; RNA;

CATALYSIS;

MAGNESIUM ION; NUCLEOPHILE; RIBOZYME; RNA;

ARTICLE; BASE PAIRING; CATALYSIS; CRYSTAL STRUCTURE; ENZYME ACTIVITY; HETERONUCLEAR SINGLE QUANTUM COHERENCE; HYDROGEN BOND; IN VITRO STUDY; MOLECULAR MODEL; MUTATIONAL ANALYSIS; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; POINT MUTATION; PROTON NUCLEAR MAGNETIC RESONANCE; RNA CONFORMATION; RNA SPLICING; RNA STRUCTURE; STATIC ELECTRICITY; WILD TYPE; X RAY CRYSTALLOGRAPHY;

BASE SEQUENCE; BINDING SITES; MAGNESIUM; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; RNA, CATALYTIC;

EID: 84875425784     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja311868t     Document Type: Article

References (34)

1. Will, C. L.; Lührmann, R. Cold Spring Harbor Persp. Biol. 2011, 3, a003707
2. Pyle, A. M.; Lambowitz, A. M. The RNA World, 3 rd ed.; Cold Spring Harbor Laboratory Press: Cold Sping Harbor, NY, 2006.
3. Cech, T. R. Cell 1986, 44, 207-210
4. Sharp, P. A. Cell 1985, 42, 397-400
5. Guthrie, C. Science 1991, 253, 157-163
6. Valadkhan, S.; Manley, J. L. Nature 2001, 413, 701-707
7. Tuschl, T.; Sharp, P. A.; Bartel, D. P. RNA 2001, 7, 29-43
8. Toor, N.; Keating, K. S.; Taylor, S. D.; Pyle, A. M. Science 2008, 320, 77-82
9. Chan, R. T.; Robart, A. R.; Rajashankar, K. R.; Pyle, A. M.; Toor, N. Nat. Struct. Mol. Biol. 2012, 10, 555-557
10. Tuschl, T.; Sharp, P.; Bartel, D. P. EMBO J. 1998, 17, 2637-2650
11. Hennig, M.; Williamson, J. R. Nucleic Acids Res. 2000, 28, 1585-1593
12. Dingley, A. J.; Grzesiek, S. J. Am. Chem. Soc. 1998, 120, 8293-8297
13. Sklenar, V.; Dieckmann, T.; Butcher, S. E.; Feigon, J. J. Magn. Reson. 1998, 130, 119-124
14. Hu, W. D.; Kakalis, L. T.; Jiang, L. C.; Jiang, F.; Ye, X. M.; Majumdar, A. J. Biomol. NMR 1998, 12, 559-564
15. Zwahlen, C.; Legault, P.; Vincent, S. J. F.; Greenblatt, J.; Konrat, R.; Kay, L. E. J. Am. Chem. Soc. 1997, 119, 6711-6721
16. Brünger, A. T.; Adams, P. D.; Clore, G. M.; DeLano, W. L.; Gros, P.; Grosse-Kunstleve, R. W.; Jiang, J. S.; Kuszewski, J.; Nilges, M.; Pannu, N. S.; Read, R. J.; Rice, L. M.; Simonson, T.; Warren, G. L. Acta Crystallogr. Sect. D: Biol. Crystallogr. 1998, 54, 905-921
17. Linge, J. P.; Habeck, M.; Rieping, W.; Nilges, M. Bioinformatics 2003, 19, 315-316
18. Ohlenschläger, O.; Haumann, S.; Ramachandran, R.; Görlach, M. J. Biomol. NMR 2008, 42, 139-142
19. Case, D. A.; Darden, T. A.; Cheatham, III, T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Walker, R. C.; Zhang, W.; Merz, K. M.; AMBER 11; University of California, San Francisco, 2010.
20. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926
21. Hashem, Y.; Auffinger, P. Methods (San Diego, Calif.) 2009, 47, 187-197
22. Pernot, P.; Theveneau, P.; Giraud, T.; Fernandes, R. N.; Nurizzo, D.; Spruce, D.; Surr, J.; McSweeney, S.; Round, A.; Felisaz, F.; Foedinger, L.; Gobbo, A.; Huet, J.; Villard, C.; Cipriani, F. J. Phys.: Conf. Ser. 2010, 247, 12009
23. Konarev, P. V; Volkov, V. V; Sokolova, A. V; Koch, M. H. J.; Svergun, D. I. J. Appl. Crystallogr. 2003, 36, 1277-1282
24. Leontis, N. B.; Westhof, E. Comp. Funct. Genom. 2002, 3, 518-524
25. Pearlman, D. a.; Case, D. a.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E.; DeBolt, S.; Ferguson, D.; Seibel, G.; Kollman, P.; Cheatham Iii, T. E. Comput. Phys. Commun. 1995, 91, 1-41
26. Auffinger, P.; Bielecki, L.; Westhof, E. Structure 2004, 12, 379-388
27. Valadkhan, S.; Manley, J. L. RNA 2009, 15, 4-7
28. Smith, A. J.; Konarska, M. M. RNA 2009, 15, 1-3
29. Madhani, H. D.; Guthrie, C. Annu. Rev. Genet. 1994, 28, 1-26
30. Sontheimer, E. J.; Steiz, J. A. Science 1993, 262, 1989-1996
31. Parker, R.; Siciliano, P. G.; Guthrie, C. Cell 1987, 49, 229-239
32. Nilsen, T. W. In RNA structure and function; Simons, R. W.; Grunberg-Manago, M., Eds.; Cold Spring Harbor Laboratory Press:: Cold Spring Harbor, NY, 1998; pp 303-357.
33. Moore, M. J.; Query, C. C.; Sharp, P. A. In The RNA world; Gestland, R. F.; Atkins, J. F., Eds.; Cold Spring Harbor Laboratory Press:: Cold Spring Harbor, NY, 1993; pp 303-357.
34. Steiz, T. A.; Steiz, J. A. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 6498-6502