The structural and functional uniqueness of the glmS ribozyme

Progress in Molecular Biology and Translational Science

Volumn 120, Issue , 2013, Pages 173-193

  Soukup, Juliane K ^a  

^a CREIGHTON UNIVERSITY   (United States)

Author keywords

Acid base catalysis; Coenzyme; Riboswitch; Ribozyme; Self cleavage

Indexed keywords

ANTIBIOTIC AGENT; GLMS RIBOZYME; GLUCOSE 6 PHOSPHATE; MESSENGER RNA; METAL ION; NUCLEIC ACID BASE; PHOSPHATE; PHOSPHOROTHIOIC ACID; RIBONUCLEASE E; RIBOZYME; UNCLASSIFIED DRUG;

ALLOSTERISM; ARTICLE; BACILLUS ANTHRACIS; BACTERIAL GROWTH; CATALYSIS; CLOSTRIDIUM DIFFICILE; COENZYME; COMPETITIVE INHIBITION; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; GENETIC REGULATION; GRAM POSITIVE BACTERIUM; HYDROGEN BOND; LIGAND BINDING; MOLECULAR DYNAMICS; NONHUMAN; OPEN READING FRAME; PH; PROTEIN CLEAVAGE; PROTEIN SECONDARY STRUCTURE; PROTON TRANSPORT; RIBOSWITCH; RNA CONFORMATION; RNA STRUCTURE; TRANSCRIPTION TERMINATION; X RAY CRYSTALLOGRAPHY;

ACID-BASE CATALYSIS; COENZYME; RIBOSWITCH; RIBOZYME; SELF-CLEAVAGE;

BACTERIAL PROTEINS; PROTEIN CONFORMATION; RNA, CATALYTIC; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84896697569     PISSN: 18771173     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-381286-5.00005-6     Document Type: Chapter

References (46)

1. I.T. Paulsen, L. Banerjei, and G.S. Myers Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis Science 299 5615 2003 2071 2074
2. W.C. Winkler, A. Nahvi, A. Roth, J.A. Collins, and R.R. Breaker Control of gene expression by a natural metabolite-responsive ribozyme Nature 428 6980 2004 281 286
3. E. Nudler, and A.S. Mironov The riboswitch control of bacterial metabolism Trends Biochem. Sci 29 1 2004 11 17
4. W.C. Winkler, and R.R. Breaker Regulation of bacterial gene expression by riboswitches Annu. Rev. Microbiol 59 2005 487 517
5. J.A. Collins, I. Irnov, S. Baker, and W.C. Winkler Mechanism of mRNA destabilization by the glmS ribozyme Genes Dev 21 24 2007 3356 3368
6. T.J. McCarthy, M.A. Plog, S.A. Floy, J.A. Jansen, J.K. Soukup, and G.A. Soukup Ligand requirements for glmS ribozyme self-cleavage Chem. Biol 12 11 2006 1221 1226
7. S. Griffiths-Jones, S. Moxon, M. Marshall, A. Khanna, S.R. Eddy, and A. Bateman Rfam: annotating noncoding RNAs in complete genomes Nucleic Acids Res 33 database issue 2005 D121 D124
8. S. Griffiths-Jones, A. Bateman, M. Marshall, A. Khanna, and S.R. Eddy Rfam: an RNA family database Nucleic Acids Res 31 1 2003 439 441
9. J.E. Barrick, K.A. Corbino, and W.C. Winkler New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control Proc. Natl. Acad. Sci. USA 101 17 2004 6421 6426
10. S. Milewski Glucosamine-6-phosphate synthase: the multi-facets enzyme Biochim. Biophys. Acta 1597 2 2002 173 192
11. M.-A. Badet-Denisot, L. Rene, and B. Badet Mechanistic investigations on glucosamine-6-phosphate synthase Bull. Soc. Chim. Fr 130 1993 249 255
12. D.J. Klein, and A.R. Ferré-D'Amaré Structural basis of glmS ribozyme activation by glucosamine-6-phosphate Science 313 5794 2006 1752 1756
13. J.C. Cochrane, S.V. Lipchock, and S.A. Strobel Structural investigation of the glmS ribozyme bound to its catalytic cofactor Chem. Biol 14 1 2007 97 105
14. D.J. Klein, M.D. Been, and A.R. Ferré-D'Amaré Essential role of an active-site guanine in glmS ribozyme catalysis J. Am. Chem. Soc 129 48 2007 14858 14859
15. D.J. Klein, S.R. Wilkinson, M.D. Been, and A.R. Ferré- D'Amaré Requirement of helix P2.2 and nucleotide G1 for positioning the cleavage site and cofactor of the glmS ribozyme J. Mol. Biol 373 1 2007 178 189
16. R.A. Tinsley, J.R. Furchak, and N.G. Walter Trans-acting glmS catalytic riboswitch: locked and loaded RNA 13 4 2007 468 477
17. J.C. Cochrane, S.V. Lipchock, K.D. Smith, and S.A. Strobel Structural and chemical basis for glucosamine-6-phosphate binding and activation of the glmS ribozyme Biochemistry 48 15 2009 3239 3246
18. C.E. Lünse, M.S. Schmidt, V. Wittmann, and G. Mayer Carba-sugars activate the glmS-riboswitch of Staphylococcus aureus ACS Chem. Biol 6 7 2011 675 678
19. J. Lim, B.C. Grove, A. Roth, and R.R. Breaker Characteristics of ligand recognition by a glmS self-cleaving ribozyme Angew. Chem. Int. Ed. Engl 45 40 2006 6689 6693
20. J.C. Cochrane, and S.A. Strobel Riboswitch effectors as protein enzyme cofactors RNA 14 6 2008 993 1002
21. P.Y. Watson, and M.J. Fedor The glmS riboswitch integrates signals from activating and inhibitory metabolites in vivo Nat. Struct. Mol. Biol 18 3 2011 359 363
22. E.F. Pettersen, T.D. Goddard, and C.C. Huang UCSF Chimera - a visualization system for exploratory research and analysis J. Comput. Chem 25 13 2004 1605 1612
23. Chimera home page: http://www.cgl.ucsf.edu/chimera. Accessed 30.06.2013.
24. M.F. Sanner, A.J. Olson, and J.C. Spehner Reduced surface: an efficient way to compute molecular surfaces Biopolymers 38 3 1996 305 320
25. S.R. Wilkinson, and M.D. Been A pseudoknot in the 3' non-core region of the glmS ribozyme enhances self-cleavage activity RNA 11 12 2005 1788 1794
26. G.A. Soukup Core requirements for glmS ribozyme self-cleavage reveal a putative pseudoknot structure Nucleic Acids Res 34 3 2006 968 975
27. J.A. Jansen, T.J. McCarthy, G.A. Soukup, and J.K. Soukup Backbone and nucleobase contacts to glucosamine-6-phosphate in the glmS ribozyme Nat. Struct. Mol. Biol 13 6 2006 517 523
28. K.J. Hampel, and M.M. Tinsley Evidence for preorganization of the glmS ribozyme ligand binding pocket Biochemistry 45 25 2006 7861 7871
29. K.M. Brooks, and K.J. Hampel A rate-limiting conformational step in the catalytic pathway of the glmS ribozyme Biochemistry 48 24 2009 5669 5678
30. A. Roth, A. Nahvi, M. Lee, I. Jona, and R.R. Breaker Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions RNA 12 4 2006 607 619
31. K. Klawuhn, J.A. Jansen, J. Souchek, G.A. Soukup, and J.K. Soukup Analysis of metal ion dependence in glmS ribozyme self-cleavage and coenzyme binding Chembiochem 11 18 2010 2567 2571
32. R. Jou, and J.A. Cowan Ribonuclease H activation by inert transition-metal complexes. Mechanistic probes for metallocofactors: insights on the metallobiochemistry of divalent magnesium ion J. Am. Chem. Soc 113 17 1991 6685 6686
33. 2 +(aq) binding sites J. Inorg. Biochem 49 3 1993 171 175
34. K.M. Brooks, and K.J. Hampel Rapid steps in the glmS ribozyme catalytic pathway: cation and ligand requirements Biochemistry 50 13 2011 2424 2433
35. K.H. Link, L. Guo, and R.R. Breaker Examination of the structural and functional versatility of glmS ribozymes by using in vitro selection Nucleic Acids Res 34 17 2006 4968 4975
36. a toward neutrality Biochemistry 50 33 2011 7236 7242
37. P. Banás, N.G. Walter, J. Sponer, and M. Otyepka Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics J. Phys. Chem. B 114 26 2010 8701 8712
38. Y. Xin, and D. Hamelberg Deciphering the role of glucosamine-6-phosphate in the riboswitch action of glmS ribozyme RNA 16 12 2010 2455 2463
39. B. Gong, D.J. Klein, A.R. Ferre-D'Amare, and P.R. Carey The glmS ribozyme tunes the catalytically critical pK(a) of its coenzyme glucosamine-6-phosphate J. Am. Chem. Soc 133 36 2011 14188 14191
40. J. Viladoms, L.G. Scott, and M.J. Fedor An active-site guanine participates in glmS ribozyme catalysis in its protonated state J. Am. Chem. Soc 133 45 2011 18388 18396
41. J. Viladoms, and M.J. Fedor The glmS ribozyme cofactor is a general acid-base catalyst J. Am. Chem. Soc 134 46 2012 19043 19049
42. J.J. Posakony, and A.R. Ferre-D'Amare Glucosamine and glucosamine-6-phosphate derivatives: catalytic cofactor analogues for the glmS ribozyme J Org Chem 78 10 2013 4730 4743
43. G.A. Soukup, and J.K. Soukup Structure and mechanism of the glmS ribozyme N. Walter, S.A. Woodson, R.T. Batey, Non-Protein Coding RNAs - Springer Series in Biophysics 2009 Springer Berlin, Germany 129 143
44. P.C. Bevilacqua Mechanistic considerations for general acid-base catalysis by RNA: revisiting the mechanism for the hairpin ribozyme Biochemistry 42 8 2003 2259 2265
45. N. Sudarsan, J.K. Wickiser, S. Nakamura, M.S. Ebert, and R.R. Breaker An mRNA structure in bacteria that controls gene expression by binding lysine Genes Dev 17 21 2003 2688 2697
46. N. Sudarsan, S. Cohen-Chalamish, S. Nakamura, G.M. Emilsson, and R.R. Breaker Thiamine pyrophosphate riboswitches are targets for the antimicrobial compound pyrithiamine Chem. Biol 12 12 2005 1325 1335