Requirement of Helix P2.2 and Nucleotide G1 for Positioning the Cleavage Site and Cofactor of the glmS Ribozyme

Journal of Molecular Biology

Volumn 373, Issue 1, 2007, Pages 178-189

  Klein, Daniel J ^a   Wilkinson, Sara R ^b   Been, Michael D ^b   Ferré D'Amaré, Adrian R ^a  

^a Fred Hutchinson Cancer Research Center   (United States)

^b DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

glmS ribozyme; glucosamine 6 phosphate; riboswitch; ribozyme cofactor; trans acting ribozyme

Indexed keywords

RIBOZYME;

ARTICLE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME CONFORMATION; ENZYME STRUCTURE; NONHUMAN; PRIORITY JOURNAL; RNA ANALYSIS; STRUCTURE ANALYSIS; THERMOANAEROBACTER; THERMOANAEROBACTER TENGCONGENSIS;

THERMOANAEROBACTER TENGCONGENSIS;

EID: 34548591567     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.07.062     Document Type: Article

References (24)

1. Barrick J.E., Corbino K.A., Winkler W.C., Nahvi A., Mandal M., Collins J., et al. New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc. Natl Acad. Sci. USA 101 (2004) 6421-6426
2. Winkler W.C., Nahvi A., Roth A., Collins J.A., and Breaker R.R. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428 (2004) 281-286
3. Klein D.J., and Ferré-D'Amaré A.R. Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science 313 (2006) 1752-1756
4. Edwards T.E., Klein D.J., and Ferré-D'Amaré A.R. Riboswitches: small-molecule recognition by gene regulatory RNAs. Curr. Opin. Struct. Biol. 17 (2006) 273-279
5. Hampel K.J., and Tinsley M.M. Evidence for preorganization of the glmS ribozyme ligand binding pocket. Biochemistry 45 (2006) 7861-7871
6. Tinsley R.A., Furchak J.R., and Walter N.G. Trans-acting glmS catalytic riboswitch: locked and loaded. RNA 13 (2007) 468-477
7. McCarthy T.J., Plog M.A., Floy S.A., Jansen J.A., Soukup J.K., and Soukup G.A. Ligand requirements for glmS ribozyme self-cleavage. Chem. Biol. 12 (2005) 1221-1226
8. Lim J., Grove B.C., Roth A., and Breaker R.R. Characteristics of ligand recognition by a glmS self-cleaving ribozyme. Angew Chem. Int. Ed. Engl. 45 (2006) 6689-6693
9. Soukup G.A. Core requirements for glmS ribozyme self-cleavage reveal a putative pseudoknot structure. Nucl. Acids Res. 34 (2006) 968-975
10. Cochrane J.C., Lipchock S.V., and Strobel S.A. Structural investigation of the GlmS ribozyme bound to its catalytic cofactor. Chem. Biol. 14 (2007) 97-105
11. Nissen P., Ippolito J.A., Ban N., Moore P.B., and Steitz T.A. RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc. Natl Acad. Sci. USA 98 (2001) 4899-4903
12. Wilkinson S.R., and Been M.D. A pseudoknot in the 3′ non-core region of the glmS ribozyme enhances self-cleavage activity. RNA 11 (2005) 1788-1794
13. Ferré-D'Amaré A.R., Zhou K., and Doudna J.A. Crystal structure of a hepatitis delta virus ribozyme. Nature 395 (1998) 567-574
14. Wadkins T.S., Perrotta A.T., Ferré-D'Amaré A.R., Doudna J.A., and Been M.D. A nested double-pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta viurs ribozymes. RNA 5 (1999) 720-727
15. Serganov A., Keiper S., Malinina L., Tereshko V., Skripkin E., Hobartner C., et al. Structural Basis for Diels-Alder ribozyme catalyzed carbon-carbon bond formation. Nature Struct. Mol. Biol. 12 (2005) 218-224
16. Pitt J.N., and Ferré-D'Amaré A.R. How RNA closes a Diel. Nature Struct. Mol. Biol. 12 (2005) 206-208
17. Roth A., Nahvi A., Lee M., Jona I., and Breaker R.R. Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions. RNA 12 (2006) 607-619
18. Bass B.L., and Cech T.R. Specific interaction between the self-splicing RNA of Tetrahymena and its guanosine substrate: implications for biological catalysis by RNA. Nature 308 (1984) 820-826
19. Jansen J.A., McCarthy T.J., Soukup G.A., and Soukup J.K. Backbone and nucleobase contacts to glucosamine-6-phosphate in the glmS ribozyme. Nature Struct. Mol. Biol. 13 (2006) 517-523
20. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 (1997) 307-326
21. Brünger A.T., Adams P.D., Clore G.M., Gros P., Grosse-Kunstleve R.W., Jiang J.-S., et al. Crystallography and NMR system: a new software system for macromolecular structure determination. Acta Crystallog. sect. D 54 (1998) 905-921
22. Davanloo P., Rosenberg A.H., Dunn J.J., and Studier F.W. Cloning and expression of the gene for bacteriophage T7 RNA polymerase. Proc. Natl Acad. Sci. USA 81 (1984) 2035-2039
23. Kunkel T.A., Roberts J.D., and Zakour R.A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol. 154 (1987) 367-382
24. Perrotta A.T., and Been M.D. A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta virus RNA. Nature 350 (1991) 434-436