Skip to main content
PMC home page
RNA logoLink to RNA
. 2002 Apr;8(4):440–451. doi: 10.1017/s1355838202026043

Solution structure of an RNA fragment with the P7/P9.0 region and the 3'-terminal guanosine of the tetrahymena group I intron.

Aya Kitamura 1, Yutaka Muto 1, Satoru Watanabe 1, Insil Kim 1, Takuhiro Ito 1, Yoichi Nishiya 1, Kensaku Sakamoto 1, Takashi Ohtsuki 1, Gota Kawai 1, Kimitsuna Watanabe 1, Kazumi Hosono 1, Hiroshi Takaku 1, Etsuko Katoh 1, Toshimasa Yamazaki 1, Tan Inoue 1, Shigeyuki Yokoyama 1
PMCID: PMC1370267  PMID: 11991639

Abstract

In the second step of the two consecutive transesterifications of the self-splicing reaction of the group I intron, the conserved guanosine at the 3' terminus of the intron (omegaG) binds to the guanosine-binding site (GBS) in the intron. In the present study, we designed a 22-nt model RNA (GBS/omegaG) including the GBS and omegaG from the Tetrahymena group I intron, and determined the solution structure by NMR methods. In this structure, omegaG is recognized by the formation of a base triple with the G264 x C311 base pair, and this recognition is stabilized by the stacking interaction between omegaG and C262. The bulged structure at A263 causes a large helical twist angle (40 +/- 80) between the G264 x C311 and C262 x G312 base pairs. We named this type of binding pocket with a bulge and a large twist, formed on the major groove, a "Bulge-and-Twist" (BT) pocket. With another twist angle between the C262 x G312 and G413 x C313 base pairs (45 +/- 100), the axis of GBS/omegaG is kinked at the GBS region. This kinked axis superimposes well on that of the corresponding region in the structure model built on a 5.0 A resolution electron density map (Golden et al., Science, 1998, 282:345-358). This compact structure of the GBS is also consistent with previous biochemical studies on group I introns. The BT pockets are also found in the arginine-binding site of the HIV-TAR RNA, and within the 16S rRNA and the 23S rRNA.

Full Text

The Full Text of this article is available as a PDF (19.9 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Ban N., Nissen P., Hansen J., Moore P. B., Steitz T. A. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science. 2000 Aug 11;289(5481):905–920. doi: 10.1126/science.289.5481.905. [DOI] [PubMed] [Google Scholar]
  2. Been M. D., Perrotta A. T. Group I intron self-splicing with adenosine: evidence for a single nucleoside-binding site. Science. 1991 Apr 19;252(5004):434–437. doi: 10.1126/science.2017681. [DOI] [PubMed] [Google Scholar]
  3. Brodsky A. S., Williamson J. R. Solution structure of the HIV-2 TAR-argininamide complex. J Mol Biol. 1997 Apr 4;267(3):624–639. doi: 10.1006/jmbi.1996.0879. [DOI] [PubMed] [Google Scholar]
  4. Burke J. M. Molecular genetics of group I introns: RNA structures and protein factors required for splicing--a review. Gene. 1988 Dec 20;73(2):273–294. doi: 10.1016/0378-1119(88)90493-3. [DOI] [PubMed] [Google Scholar]
  5. Calnan B. J., Tidor B., Biancalana S., Hudson D., Frankel A. D. Arginine-mediated RNA recognition: the arginine fork. Science. 1991 May 24;252(5009):1167–1171. doi: 10.1126/science.252.5009.1167. [DOI] [PubMed] [Google Scholar]
  6. Cate J. H., Gooding A. R., Podell E., Zhou K., Golden B. L., Kundrot C. E., Cech T. R., Doudna J. A. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science. 1996 Sep 20;273(5282):1678–1685. doi: 10.1126/science.273.5282.1678. [DOI] [PubMed] [Google Scholar]
  7. Cech T. R., Herschlag D., Piccirilli J. A., Pyle A. M. RNA catalysis by a group I ribozyme. Developing a model for transition state stabilization. J Biol Chem. 1992 Sep 5;267(25):17479–17482. [PubMed] [Google Scholar]
  8. Colmenarejo G., Tinoco I., Jr Structure and thermodynamics of metal binding in the P5 helix of a group I intron ribozyme. J Mol Biol. 1999 Jul 2;290(1):119–135. doi: 10.1006/jmbi.1999.2867. [DOI] [PubMed] [Google Scholar]
  9. Couture S., Ellington A. D., Gerber A. S., Cherry J. M., Doudna J. A., Green R., Hanna M., Pace U., Rajagopal J., Szostak J. W. Mutational analysis of conserved nucleotides in a self-splicing group I intron. J Mol Biol. 1990 Oct 5;215(3):345–358. doi: 10.1016/s0022-2836(05)80356-0. [DOI] [PubMed] [Google Scholar]
  10. Golden B. L., Gooding A. R., Podell E. R., Cech T. R. A preorganized active site in the crystal structure of the Tetrahymena ribozyme. Science. 1998 Oct 9;282(5387):259–264. doi: 10.1126/science.282.5387.259. [DOI] [PubMed] [Google Scholar]
  11. Inoue T., Sullivan F. X., Cech T. R. New reactions of the ribosomal RNA precursor of Tetrahymena and the mechanism of self-splicing. J Mol Biol. 1986 May 5;189(1):143–165. doi: 10.1016/0022-2836(86)90387-6. [DOI] [PubMed] [Google Scholar]
  12. Jucker F. M., Heus H. A., Yip P. F., Moors E. H., Pardi A. A network of heterogeneous hydrogen bonds in GNRA tetraloops. J Mol Biol. 1996 Dec 20;264(5):968–980. doi: 10.1006/jmbi.1996.0690. [DOI] [PubMed] [Google Scholar]
  13. Kellogg G. W., Schweitzer B. I. Two- and three-dimensional 31P-driven NMR procedures for complete assignment of backbone resonances in oligodeoxyribonucleotides. J Biomol NMR. 1993 Sep;3(5):577–595. doi: 10.1007/BF00174611. [DOI] [PubMed] [Google Scholar]
  14. Kim I., Muto Y., Inoue M., Watanabe S., Kitamura A., Yokoyama S., Hosono K., Takaku H., Ono A., Kainosho M. NMR analysis of the hydrogen bonding interactions of the RNA-binding domains of the Drosophila sex-lethal protein with target RNA fragments with site-specific [3-15N]uridine substitutions. Nucleic Acids Res. 1997 Apr 15;25(8):1565–1569. doi: 10.1093/nar/25.8.1565. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Lehnert V., Jaeger L., Michel F., Westhof E. New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme. Chem Biol. 1996 Dec;3(12):993–1009. doi: 10.1016/s1074-5521(96)90166-0. [DOI] [PubMed] [Google Scholar]
  16. Luebke K. J., Landry S. M., Tinoco I., Jr Solution conformation of a five-nucleotide RNA bulge loop from a group I intron. Biochemistry. 1997 Aug 19;36(33):10246–10255. doi: 10.1021/bi9701540. [DOI] [PubMed] [Google Scholar]
  17. Michel F., Hanna M., Green R., Bartel D. P., Szostak J. W. The guanosine binding site of the Tetrahymena ribozyme. Nature. 1989 Nov 23;342(6248):391–395. doi: 10.1038/342391a0. [DOI] [PubMed] [Google Scholar]
  18. Michel F., Westhof E. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J Mol Biol. 1990 Dec 5;216(3):585–610. doi: 10.1016/0022-2836(90)90386-Z. [DOI] [PubMed] [Google Scholar]
  19. Ohtsuki T., Kawai G., Watanabe K. Stable isotope-edited NMR analysis of Ascaris suum mitochondrial tRNAMet having a TV-replacement loop. J Biochem. 1998 Jul;124(1):28–34. doi: 10.1093/oxfordjournals.jbchem.a022092. [DOI] [PubMed] [Google Scholar]
  20. Orita M., Nishikawa F., Shimayama T., Taira K., Endo Y., Nishikawa S. High-resolution NMR study of a synthetic oligoribonucleotide with a tetranucleotide GAGA loop that is a substrate for the cytotoxic protein, ricin. Nucleic Acids Res. 1993 Dec 11;21(24):5670–5678. doi: 10.1093/nar/21.24.5670. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Ortoleva-Donnelly L., Szewczak A. A., Gutell R. R., Strobel S. A. The chemical basis of adenosine conservation throughout the Tetrahymena ribozyme. RNA. 1998 May;4(5):498–519. doi: 10.1017/s1355838298980086. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Piccirilli J. A., Vyle J. S., Caruthers M. H., Cech T. R. Metal ion catalysis in the Tetrahymena ribozyme reaction. Nature. 1993 Jan 7;361(6407):85–88. doi: 10.1038/361085a0. [DOI] [PubMed] [Google Scholar]
  23. Puglisi J. D., Tan R., Calnan B. J., Frankel A. D., Williamson J. R. Conformation of the TAR RNA-arginine complex by NMR spectroscopy. Science. 1992 Jul 3;257(5066):76–80. doi: 10.1126/science.1621097. [DOI] [PubMed] [Google Scholar]
  24. Pyle A. M., Murphy F. L., Cech T. R. RNA substrate binding site in the catalytic core of the Tetrahymena ribozyme. Nature. 1992 Jul 9;358(6382):123–128. doi: 10.1038/358123a0. [DOI] [PubMed] [Google Scholar]
  25. Russell R., Herschlag D. Specificity from steric restrictions in the guanosine binding pocket of a group I ribozyme. RNA. 1999 Feb;5(2):158–166. doi: 10.1017/s1355838299981839. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Shan S. o., Yoshida A., Sun S., Piccirilli J. A., Herschlag D. Three metal ions at the active site of the Tetrahymena group I ribozyme. Proc Natl Acad Sci U S A. 1999 Oct 26;96(22):12299–12304. doi: 10.1073/pnas.96.22.12299. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Smith J. S., Nikonowicz E. P. NMR structure and dynamics of an RNA motif common to the spliceosome branch-point helix and the RNA-binding site for phage GA coat protein. Biochemistry. 1998 Sep 29;37(39):13486–13498. doi: 10.1021/bi981558a. [DOI] [PubMed] [Google Scholar]
  28. Strobel S. A., Ortoleva-Donnelly L. A hydrogen-bonding triad stabilizes the chemical transition state of a group I ribozyme. Chem Biol. 1999 Mar;6(3):153–165. doi: 10.1016/S1074-5521(99)89007-3. [DOI] [PubMed] [Google Scholar]
  29. Szewczak A. A., Ortoleva-Donnelly L., Ryder S. P., Moncoeur E., Strobel S. A. A minor groove RNA triple helix within the catalytic core of a group I intron. Nat Struct Biol. 1998 Dec;5(12):1037–1042. doi: 10.1038/4146. [DOI] [PubMed] [Google Scholar]
  30. Szewczak A. A., Ortoleva-Donnelly L., Zivarts M. V., Oyelere A. K., Kazantsev A. V., Strobel S. A. An important base triple anchors the substrate helix recognition surface within the Tetrahymena ribozyme active site. Proc Natl Acad Sci U S A. 1999 Sep 28;96(20):11183–11188. doi: 10.1073/pnas.96.20.11183. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Varani G., Cheong C., Tinoco I., Jr Structure of an unusually stable RNA hairpin. Biochemistry. 1991 Apr 2;30(13):3280–3289. doi: 10.1021/bi00227a016. [DOI] [PubMed] [Google Scholar]
  32. Wang J. F., Cech T. R. Tertiary structure around the guanosine-binding site of the Tetrahymena ribozyme. Science. 1992 Apr 24;256(5056):526–529. doi: 10.1126/science.1315076. [DOI] [PubMed] [Google Scholar]
  33. Watanabe S., Kawai G., Muto Y., Watanabe K., Inoue T., Yokoyama S. An RNA fragment consisting of the P7 and P9.0 stems and the 3'-terminal guanosine of the Tetrahymena group I intron. Nucleic Acids Res. 1996 Apr 1;24(7):1337–1344. doi: 10.1093/nar/24.7.1337. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Weinstein L. B., Jones B. C., Cosstick R., Cech T. R. A second catalytic metal ion in group I ribozyme. Nature. 1997 Aug 21;388(6644):805–808. doi: 10.1038/42076. [DOI] [PubMed] [Google Scholar]
  35. Wimberly B. T., Brodersen D. E., Clemons W. M., Jr, Morgan-Warren R. J., Carter A. P., Vonrhein C., Hartsch T., Ramakrishnan V. Structure of the 30S ribosomal subunit. Nature. 2000 Sep 21;407(6802):327–339. doi: 10.1038/35030006. [DOI] [PubMed] [Google Scholar]
  36. Yarus M. A specific amino acid binding site composed of RNA. Science. 1988 Jun 24;240(4860):1751–1758. doi: 10.1126/science.3381099. [DOI] [PubMed] [Google Scholar]
  37. Yarus M., Illangesekare M., Christian E. An axial binding site in the Tetrahymena precursor RNA. J Mol Biol. 1991 Dec 20;222(4):995–1012. doi: 10.1016/0022-2836(91)90590-3. [DOI] [PubMed] [Google Scholar]
  38. Yarus M., Majerfeld I. Co-optimization of ribozyme substrate stacking and L-arginine binding. J Mol Biol. 1992 Jun 20;225(4):945–949. doi: 10.1016/0022-2836(92)90095-2. [DOI] [PubMed] [Google Scholar]
  39. Yarus M. Specificity of arginine binding by the Tetrahymena intron. Biochemistry. 1989 Feb 7;28(3):980–988. doi: 10.1021/bi00429a010. [DOI] [PubMed] [Google Scholar]
  40. Zeffman A., Hassard S., Varani G., Lever A. The major HIV-1 packaging signal is an extended bulged stem loop whose structure is altered on interaction with the Gag polyprotein. J Mol Biol. 2000 Apr 7;297(4):877–893. doi: 10.1006/jmbi.2000.3611. [DOI] [PubMed] [Google Scholar]

Articles from RNA are provided here courtesy of The RNA Society

RESOURCES