Linking the group II intron catalytic domains: Tertiary contacts and structural features of domain 3

EMBO Journal

Volumn 24, Issue 22, 2005, Pages 3906-3916

  Fedorova, Olga ^a   Pyle, Anna Marie ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

Enzymology; Ribozyme; RNA folding; Splicing; Tertiary structure

Indexed keywords

FUNCTIONAL GROUP; NUCLEOTIDE DERIVATIVE; RIBOZYME;

ARTICLE; CATALYSIS; GENE STRUCTURE; INTRON; MUTATION; NUCLEIC ACID ANALYSIS; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DOMAIN; RNA SPLICING;

CATALYTIC DOMAIN; DNA MUTATIONAL ANALYSIS; INTRONS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEOTIDES; RNA, CATALYTIC;

EID: 27844592623     PISSN: 02614189     EISSN: 14602075     Source Type: Journal    
DOI: 10.1038/sj.emboj.7600852     Document Type: Article

References (35)

1. Abramovitz DL, Friedman RA, Pyle AM (1996) Catalytic role of 2′-hydroxyl groups within a group II intron active site. Science 271: 1410-1413
2. Abramovitz DL, Pyle AM (1997) Remarkable morphological variability of a common RNA folding motif: the GNRA tetraloop-receptor interaction. J Mol Biol 266: 493-506
3. Boudvillain M, DeLencastre A, Pyle AM (2000) A new RNA tertiary interaction that links active-site domains of a group II intron and anchors them at the site of catalysis. Nature 406: 315-318
4. Boudvillain M, Pyle AM (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: 7091-7104
5. Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Kundrot CE, Cech TR, Doudna JA (1996a) Crystal structure of a group I ribozyme domain reveals principles of higher order RNA folding. Science 273: 1678-1685
6. Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Szewczak AA, Kundrot CE, Cech TR, Doudna JA (1996b) RNA tertiary structure mediation by adenosine platforms. Science 273: 1696-1699
7. Chin K, Pyle AM (1995) Branch-point attack in group II introns is a highly reversible transesterification, providing a possible proof-reading mechanism for 5′-splice site selection. RNA 1: 391-406
8. Fedorova O, Boudvillain M, Kawaoka J, Pyle AM (2005) Nucleotide analog interference mapping and suppression: specific applications in studies of RNA tertiary structure, dynamic helicase mechanism and RNA-protein interactions. In Handbook of RNA Biochemistry, Hartmann RK, Bindereif A, Schoen A, Westhof E (eds), Vol. 1, pp 259-293. Weinheim: Wiley-VCH
9. Fedorova O, Mitros T, Pyle AM (2003) Domains 2 and 3 interact to form critical elements of the group II intron active site. J Mol Biol 330: 197-209
10. Fedorova O, Su LJ, Pyle AM (2002) Group II introns: highly specific endonucleases with modular structures and diverse catalytic functions. Methods 28: 323-335
11. Gish G, Eckstein F (1988) DNA and RNA sequence determination based on phosphorothioate chemistry. Science 240: 1520-1522
12. Griffin EA, Qin ZF, Michels WA, Pyle AM (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: 761-770
13. Huang Z, Szostak JW (1996) A simple method for 3′-labeling of RNA. Nucleic Acids Res 24: 4360-4361
14. Jarrell KA, Dietrich RC, Perlman PS (1988) Group II intron domain 5 facilitates a trans-splicing reaction. Mol Cell Biol 8: 2361-2366
15. Jestin JL, Deme E, Jacquier A (1997) Identification of structural elements critical for inter-domain interactions in a group II self-splicing intron. EMBO J 16: 2945-2954
16. Koch JL, Boulanger SC, Dib-Hajj SD, Hebbar SK, Perlman PS (1992) Group II introns deleted for multiple substructures retain self-splicing activity. Mol Cell Biol 12: 1950-1958
17. Konforti BB, Liu Q, Pyle AM (1998) A map of the binding site for catalytic domain 5 in the core of a group II intron ribozyme. EMBO J 17: 7195-7217
18. Kunkel TA, Bebenek K, McClary J (1991) Efficient site-directed mutagenesis using uracil-containing DNA. Methods Enzymol 204: 125-139
19. Legault P, Mogridge J, Kay LE, Greenblatt J (1998) NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: recognition of a GNRA fold by an arginine-rich motif. Cell 93: 289-299
20. Lehmann K, Schmidt U (2003) Group II introns: structure and catalytic versatility of large natural ribozymes. Crit Rev Biochem Mol Biol 38: 249-303
21. Leontis NB, Stombaugh J, Westhof E (2002) The non-Watson-Crick base-pairs and their associated isostericity matrices. Nucleic Acids Res 30: 3497-3531
22. Leontis NB, Westhof E (1998) Conserved geometrical base-pairing patterns in RNA. Q Rev Biophys 31: 399-455
23. Michel F, Ferat JL (1995) Structure and activities of group II introns. Annu Rev Biochem 64: 435-461
24. Michel F, Umesono K, Ozeki H (1989) Comparative and functional anatomy of group II catalytic introns - a review. Gene 82: 5-30
25. Michels WJ, Pyle AM (1995) Conversion of a group II intron into a new multiple-turnover ribozyme that selectively cleaves oligonucleotides: elucidation of reaction mechanism and structure/function relationships. Biochemistry 34: 2965-2977
26. Mikheeva S, Murray HL, Zhou H, Turczyk BM, Jarrell KA (2000) Deletion of a conserved dinucleotide inhibits the second step of group Ii intron splicing. RNA 6: 1509-1515
27. Ortoleva-Donnelly L, Sweczak AA, Gutell RR, Strobel SA (1998) The chemical basis of adenosine conservation throughout the Tetrahymena ribozyme. RNA 4: 498-519
28. 2+-dependent cross-link traps an active form of domain 3 of a self-splicing group II intron. RNA 1: 828-840
29. Pyle AM, Green JB (1994) Building a kinetic framework for group II intron ribozyme activity: quantitation of interdomain binding and reaction rate. Biochemistry 33: 2716-2725
30. Pyle AM, Lambowitz AM (2006) Group II introns: ribozymes that splice RNA and invade DNA. In The RNA World, Gesteland RF, Cech TR, Atkins JF (eds), 3rd edn, pp 469-506. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press (in press)
31. Strobel SA (1999) A chemogenetic approach to RNA function/structure analysis. Curr Opin Struct Biol 9: 346-352
32. Strobel SA (2002) Biochemical identification of A-minor motifs within RNA tertiary structure by interference analysis. Biochem Soc Trans 9: 1126-1131
33. Swisher J, Duarte C, Su L, Pyle AM (2001) Visualizing the solvent-inaccessible core of a group II intron ribozyme. EMBO J 20: 2051-2061
34. Toor N, Hausner G, Zimmerly S (2001) Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases. RNA 7: 1142-1152
35. Xiang Q, Qin PZ, Michels WJ, Freeland K, Pyle AM (1998) The sequence-specificity of a group II intron ribozyme: multiple mechanisms for promoting unusually high discrimination against mismatched targets. Biochemistry 37: 3839-3849