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Volumn 11, Issue 6, 2007, Pages 636-643

RNA catalysis: ribozymes, ribosomes, and riboswitches

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE; HISTIDINE; HYDROXYL GROUP; MESSENGER RNA; METAL ION; NUCLEIC ACID BASE; RIBOZYME; RNA POLYMERASE; TRANSFER RNA;

EID: 36549083651     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2007.09.010     Document Type: Review
Times cited : (92)

References (47)
  • 1
    • 0027184481 scopus 로고
    • A general two-metal-ion mechanism for catalytic RNA
    • Steitz T.A., and Steitz J.A. A general two-metal-ion mechanism for catalytic RNA. Proc Natl Acad Sci U S A 90 (1993) 6498-6502
    • (1993) Proc Natl Acad Sci U S A , vol.90 , pp. 6498-6502
    • Steitz, T.A.1    Steitz, J.A.2
  • 3
    • 0033600571 scopus 로고    scopus 로고
    • Probing the role of metal ions in RNA catalysis: kinetic and thermodynamic characterization of a metal ion interaction with the 2′-moiety of the guanosine nucleophile in the Tetrahymena group I ribozyme
    • Shan S.O., and Herschlag D. Probing the role of metal ions in RNA catalysis: kinetic and thermodynamic characterization of a metal ion interaction with the 2′-moiety of the guanosine nucleophile in the Tetrahymena group I ribozyme. Biochemistry 38 (1999) 10958-10975
    • (1999) Biochemistry , vol.38 , pp. 10958-10975
    • Shan, S.O.1    Herschlag, D.2
  • 4
    • 3042848954 scopus 로고    scopus 로고
    • Crystal structure of a self-splicing group I intron with both exons
    • Adams P.L., Stahley M.R., Kosek A.B., Wang J., and Strobel S.A. Crystal structure of a self-splicing group I intron with both exons. Nature 430 (2004) 45-50
    • (2004) Nature , vol.430 , pp. 45-50
    • Adams, P.L.1    Stahley, M.R.2    Kosek, A.B.3    Wang, J.4    Strobel, S.A.5
  • 5
    • 8644229237 scopus 로고    scopus 로고
    • Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site
    • Guo F., Gooding A.R., and Cech T.R. Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site. Mol Cell 16 (2004) 351-362
    • (2004) Mol Cell , vol.16 , pp. 351-362
    • Guo, F.1    Gooding, A.R.2    Cech, T.R.3
  • 6
    • 11444263264 scopus 로고    scopus 로고
    • Crystal structure of a phage Twort group I ribozyme-product complex
    • Golden B.L., Kim H., and Chase E. Crystal structure of a phage Twort group I ribozyme-product complex. Nat Struct Mol Biol 12 (2005) 82-89
    • (2005) Nat Struct Mol Biol , vol.12 , pp. 82-89
    • Golden, B.L.1    Kim, H.2    Chase, E.3
  • 7
    • 24644492337 scopus 로고    scopus 로고
    • Structural evidence for a two-metal-ion mechanism of group I intron splicing
    • X-ray crystallographic analysis of a catalytically competent group I intron reveals two magnesium ions in the active site coordinated to all the biochemically implicated ligands.
    • Stahley M.R., and Strobel S.A. Structural evidence for a two-metal-ion mechanism of group I intron splicing. Science 309 (2005) 1587-1590. X-ray crystallographic analysis of a catalytically competent group I intron reveals two magnesium ions in the active site coordinated to all the biochemically implicated ligands.
    • (2005) Science , vol.309 , pp. 1587-1590
    • Stahley, M.R.1    Strobel, S.A.2
  • 8
    • 26444490660 scopus 로고    scopus 로고
    • Crystal structure of a bacterial ribonuclease P RNA
    • Kazantsev A.V., et al. Crystal structure of a bacterial ribonuclease P RNA. Proc Natl Acad Sci U S A 102 (2005) 13392-13397
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 13392-13397
    • Kazantsev, A.V.1
  • 10
    • 0033538479 scopus 로고    scopus 로고
    • Role of metal ions in the hydrolysis reaction catalyzed by RNase P RNA from Bacillus subtilis
    • Warnecke J., Held R., Busch S., and Hartmann R. Role of metal ions in the hydrolysis reaction catalyzed by RNase P RNA from Bacillus subtilis. J Mol Biol 290 (1999) 433-445
    • (1999) J Mol Biol , vol.290 , pp. 433-445
    • Warnecke, J.1    Held, R.2    Busch, S.3    Hartmann, R.4
  • 11
    • 0034649666 scopus 로고    scopus 로고
    • Metal-ion coordination by U6 small nuclear RNA contributes to catalysis in the spliceosome
    • Yean S.L., Wuenschell G., Termini J., and Lin R.J. Metal-ion coordination by U6 small nuclear RNA contributes to catalysis in the spliceosome. Nature 408 (2000) 881-884
    • (2000) Nature , vol.408 , pp. 881-884
    • Yean, S.L.1    Wuenschell, G.2    Termini, J.3    Lin, R.J.4
  • 12
    • 34250349882 scopus 로고    scopus 로고
    • A second divalent metal ion in the group II intron reaction center
    • Splicing by group II introns employs metal ions similarly to group I introns, which suggests a catalytic paradigm for large ribozymes, possibly also exploited by the spliceosome.
    • Gordon P.M., Fong R., and Piccirilli J.A. A second divalent metal ion in the group II intron reaction center. Chem Biol 14 (2007) 607-612. Splicing by group II introns employs metal ions similarly to group I introns, which suggests a catalytic paradigm for large ribozymes, possibly also exploited by the spliceosome.
    • (2007) Chem Biol , vol.14 , pp. 607-612
    • Gordon, P.M.1    Fong, R.2    Piccirilli, J.A.3
  • 13
    • 0032192761 scopus 로고    scopus 로고
    • The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone
    • Murray J.B., Seyhan A.A., Walter N.G., Burke J.M., and Scott W.G. The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. Chem Biol 5 (1998) 587-595
    • (1998) Chem Biol , vol.5 , pp. 587-595
    • Murray, J.B.1    Seyhan, A.A.2    Walter, N.G.3    Burke, J.M.4    Scott, W.G.5
  • 14
    • 0032497521 scopus 로고    scopus 로고
    • Crystal structure of a hepatitis delta virus ribozyme
    • Ferre-D'Amare A.R., Zhou K., and Doudna J.A. Crystal structure of a hepatitis delta virus ribozyme. Nature 395 (1998) 567-574
    • (1998) Nature , vol.395 , pp. 567-574
    • Ferre-D'Amare, A.R.1    Zhou, K.2    Doudna, J.A.3
  • 15
    • 0033215448 scopus 로고    scopus 로고
    • Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme
    • Perrotta A.T., Shih I., and Been M.D. Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme. Science 286 (1999) 123-126
    • (1999) Science , vol.286 , pp. 123-126
    • Perrotta, A.T.1    Shih, I.2    Been, M.D.3
  • 16
    • 0034712097 scopus 로고    scopus 로고
    • General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme
    • Nakano S., Chadalavada D.M., and Bevilacqua P.C. General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme. Science 287 (2000) 1493-1497
    • (2000) Science , vol.287 , pp. 1493-1497
    • Nakano, S.1    Chadalavada, D.M.2    Bevilacqua, P.C.3
  • 17
    • 2442641641 scopus 로고    scopus 로고
    • A conformational switch controls hepatitis delta virus ribozyme catalysis
    • Ke A., Zhou K., Ding F., Cate J.H., and Doudna J.A. A conformational switch controls hepatitis delta virus ribozyme catalysis. Nature 429 (2004) 201-205
    • (2004) Nature , vol.429 , pp. 201-205
    • Ke, A.1    Zhou, K.2    Ding, F.3    Cate, J.H.4    Doudna, J.A.5
  • 18
    • 24644454458 scopus 로고    scopus 로고
    • General acid catalysis by the hepatitis delta virus ribozyme
    • Coupling hyperactivated substrates with mutagenesis of C76 and pH rate profiles solidifies the role of the N3 of an active site cytosine as the general acid in HDV catalysis.
    • Das S., and Piccirilli J.A. General acid catalysis by the hepatitis delta virus ribozyme. Nat Chem Biol 1 (2005) 45-52. Coupling hyperactivated substrates with mutagenesis of C76 and pH rate profiles solidifies the role of the N3 of an active site cytosine as the general acid in HDV catalysis.
    • (2005) Nat Chem Biol , vol.1 , pp. 45-52
    • Das, S.1    Piccirilli, J.A.2
  • 19
    • 0035965132 scopus 로고    scopus 로고
    • The A730 loop is an important component of the active site of the VS ribozyme
    • Lafontaine D.A., Wilson T.J., Norman D.G., and Lilley D.M. The A730 loop is an important component of the active site of the VS ribozyme. J Mol Biol 312 (2001) 663-674
    • (2001) J Mol Biol , vol.312 , pp. 663-674
    • Lafontaine, D.A.1    Wilson, T.J.2    Norman, D.G.3    Lilley, D.M.4
  • 20
    • 33746228126 scopus 로고    scopus 로고
    • Tertiary contacts distant from the active site prime a ribozyme for catalysis
    • In contrast to minimal hammerhead constructs, the crystal structure of a full-length hammerhead ribozyme presents an active site organization that is in agreement with biochemically important residues, including roles for G8 and G12.
    • Martick M., and Scott W.G. Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell 126 (2006) 309-320. In contrast to minimal hammerhead constructs, the crystal structure of a full-length hammerhead ribozyme presents an active site organization that is in agreement with biochemically important residues, including roles for G8 and G12.
    • (2006) Cell , vol.126 , pp. 309-320
    • Martick, M.1    Scott, W.G.2
  • 22
    • 34249098371 scopus 로고    scopus 로고
    • A guanine nucleobase important for catalysis by the VS ribozyme
    • Wilson T.J., McLeod A.C., and Lilley D.M. A guanine nucleobase important for catalysis by the VS ribozyme. EMBO J 26 (2007) 2489-2500
    • (2007) EMBO J , vol.26 , pp. 2489-2500
    • Wilson, T.J.1    McLeod, A.C.2    Lilley, D.M.3
  • 23
    • 2942577491 scopus 로고    scopus 로고
    • Role of an active site guanine in hairpin ribozyme catalysis probed by exogenous nucleobase rescue
    • Kuzmin Y., Da Costa C., and Fedor M. Role of an active site guanine in hairpin ribozyme catalysis probed by exogenous nucleobase rescue. J Mol Biol 340 (2004) 233-251
    • (2004) J Mol Biol , vol.340 , pp. 233-251
    • Kuzmin, Y.1    Da Costa, C.2    Fedor, M.3
  • 24
    • 0035890245 scopus 로고    scopus 로고
    • Functional involvement of G8 in the hairpin ribozyme cleavage mechanism
    • Pinard R., et al. Functional involvement of G8 in the hairpin ribozyme cleavage mechanism. EMBO J 20 (2001) 6434-6442
    • (2001) EMBO J , vol.20 , pp. 6434-6442
    • Pinard, R.1
  • 25
    • 0034637161 scopus 로고    scopus 로고
    • The structural basis of ribosome activity in peptide bond synthesis
    • Nissen P., Hansen J., Ban N., Moore P., and Steitz T. The structural basis of ribosome activity in peptide bond synthesis. Science 289 (2000) 920-930
    • (2000) Science , vol.289 , pp. 920-930
    • Nissen, P.1    Hansen, J.2    Ban, N.3    Moore, P.4    Steitz, T.5
  • 26
    • 0035979232 scopus 로고    scopus 로고
    • Analysis of mutations at residues A2451 and G2447 of 23S rRNA in the peptidyl transferase active site of the 50S ribosomal subunit
    • Thompson J., et al. Analysis of mutations at residues A2451 and G2447 of 23S rRNA in the peptidyl transferase active site of the 50S ribosomal subunit. Proc Natl Acad Sci U S A 98 (2001) 9002-9007
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 9002-9007
    • Thompson, J.1
  • 27
    • 0035942753 scopus 로고    scopus 로고
    • Ribosomal peptidyl transferase can withstand mutations at the putative catalytic nucleotide
    • Polacek N., Gaynor M., Yassin A., and Mankin A.S. Ribosomal peptidyl transferase can withstand mutations at the putative catalytic nucleotide. Nature 411 (2001) 498-501
    • (2001) Nature , vol.411 , pp. 498-501
    • Polacek, N.1    Gaynor, M.2    Yassin, A.3    Mankin, A.S.4
  • 28
    • 2542470615 scopus 로고    scopus 로고
    • The active site of the ribosome is composed of two layers of conserved nucleotides with distinct roles in peptide bond formation and peptide release
    • Youngman E.M., Brunelle J.L., Kochaniak A.B., and Green R. The active site of the ribosome is composed of two layers of conserved nucleotides with distinct roles in peptide bond formation and peptide release. Cell 117 (2004) 589-599
    • (2004) Cell , vol.117 , pp. 589-599
    • Youngman, E.M.1    Brunelle, J.L.2    Kochaniak, A.B.3    Green, R.4
  • 29
    • 27644557445 scopus 로고    scopus 로고
    • Structural insights into the roles of water and the 2′ hydroxyl of the P site tRNA in the peptidyl transferase reaction
    • Complexes of the ribosomal peptidyl transferase center in complex with A-site and P-site substrates and a chiral transition state mimic reveal specifically bound waters and the proximity of the critical 2′-OH to the α-amine and O3′ leaving group.
    • Schmeing T.M., Huang K.S., Kitchen D.E., Strobel S.A., and Steitz T.A. Structural insights into the roles of water and the 2′ hydroxyl of the P site tRNA in the peptidyl transferase reaction. Mol Cell 20 (2005) 437-448. Complexes of the ribosomal peptidyl transferase center in complex with A-site and P-site substrates and a chiral transition state mimic reveal specifically bound waters and the proximity of the critical 2′-OH to the α-amine and O3′ leaving group.
    • (2005) Mol Cell , vol.20 , pp. 437-448
    • Schmeing, T.M.1    Huang, K.S.2    Kitchen, D.E.3    Strobel, S.A.4    Steitz, T.A.5
  • 31
    • 33644959635 scopus 로고    scopus 로고
    • Regiospecificity of the peptidyl tRNA ester within the ribosomal P site
    • Huang K.S., Weinger J.S., Butler E.B., and Strobel S.A. Regiospecificity of the peptidyl tRNA ester within the ribosomal P site. J Am Chem Soc 128 (2006) 3108-3109
    • (2006) J Am Chem Soc , vol.128 , pp. 3108-3109
    • Huang, K.S.1    Weinger, J.S.2    Butler, E.B.3    Strobel, S.A.4
  • 33
    • 33645462490 scopus 로고    scopus 로고
    • Efficient ribosomal peptidyl transfer critically relies on the presence of the ribose 2′-OH at A2451 of 23S rRNA
    • Circularly permuted rRNA and ribosomal reconstitution makes it possible to perform atomic mutagenesis of functional groups in the peptidyl transferase center, including altering the 2′-OH of A2451, which is shown to be important for activity.
    • Erlacher M.D., et al. Efficient ribosomal peptidyl transfer critically relies on the presence of the ribose 2′-OH at A2451 of 23S rRNA. J Am Chem Soc 128 (2006) 4453-4459. Circularly permuted rRNA and ribosomal reconstitution makes it possible to perform atomic mutagenesis of functional groups in the peptidyl transferase center, including altering the 2′-OH of A2451, which is shown to be important for activity.
    • (2006) J Am Chem Soc , vol.128 , pp. 4453-4459
    • Erlacher, M.D.1
  • 35
    • 24644461086 scopus 로고    scopus 로고
    • Mechanism of peptide bond synthesis on the ribosome
    • Trobro S., and Aqvist J. Mechanism of peptide bond synthesis on the ribosome. Proc Natl Acad Sci U S A 102 (2005) 12395-12400
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 12395-12400
    • Trobro, S.1    Aqvist, J.2
  • 36
    • 20644434704 scopus 로고    scopus 로고
    • 2′/3′-O-Peptidyl adenosine as a general base catalyst of its own external peptidyl transfer: implications for the ribosome catalytic mechanism
    • Changalov M., et al. 2′/3′-O-Peptidyl adenosine as a general base catalyst of its own external peptidyl transfer: implications for the ribosome catalytic mechanism. Chem Biol Chem 6 (2005) 992-996
    • (2005) Chem Biol Chem , vol.6 , pp. 992-996
    • Changalov, M.1
  • 37
    • 33845604650 scopus 로고    scopus 로고
    • Mechanism of peptide bond formation on the ribosome
    • Rodnina M.V., Beringer M., and Wintermeyer W. Mechanism of peptide bond formation on the ribosome. Q Rev Biophys 39 (2006) 203-225
    • (2006) Q Rev Biophys , vol.39 , pp. 203-225
    • Rodnina, M.V.1    Beringer, M.2    Wintermeyer, W.3
  • 38
    • 0034903851 scopus 로고    scopus 로고
    • Translation: in retrospect and prospect
    • Woese C.R. Translation: in retrospect and prospect. RNA 7 (2001) 1055-1067
    • (2001) RNA , vol.7 , pp. 1055-1067
    • Woese, C.R.1
  • 39
    • 18844408328 scopus 로고    scopus 로고
    • An active role for tRNA in decoding beyond codon:anticodon pairing
    • A conformational spring in the tRNA is implicated in the mechanism of induced fit, suggesting another active role for the tRNA substrates during translation.
    • Cochella L., and Green R. An active role for tRNA in decoding beyond codon:anticodon pairing. Science 308 (2005) 1178-1180. A conformational spring in the tRNA is implicated in the mechanism of induced fit, suggesting another active role for the tRNA substrates during translation.
    • (2005) Science , vol.308 , pp. 1178-1180
    • Cochella, L.1    Green, R.2
  • 40
    • 1642586299 scopus 로고    scopus 로고
    • Control of gene expression by a natural metabolite-responsive ribozyme
    • 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
    • (2004) Nature , vol.428 , pp. 281-286
    • Winkler, W.C.1    Nahvi, A.2    Roth, A.3    Collins, J.A.4    Breaker, R.R.5
  • 41
    • 27744525243 scopus 로고    scopus 로고
    • Ligand requirements for glmS ribozyme self-cleavage
    • McCarthy T.J., et al. Ligand requirements for glmS ribozyme self-cleavage. Chem Biol 12 (2005) 1221-1226
    • (2005) Chem Biol , vol.12 , pp. 1221-1226
    • McCarthy, T.J.1
  • 43
    • 33746920364 scopus 로고    scopus 로고
    • Evidence for preorganization of the glmS ribozyme ligand binding pocket
    • Hampel K.J., and Tinsley M.M. Evidence for preorganization of the glmS ribozyme ligand binding pocket. Biochemistry 45 (2006) 7861-7871
    • (2006) Biochemistry , vol.45 , pp. 7861-7871
    • Hampel, K.J.1    Tinsley, M.M.2
  • 44
    • 33748325570 scopus 로고    scopus 로고
    • Structural basis of glmS ribozyme activation by glucosamine-6-phosphate
    • X-ray crystal structure of the glmS ribozyme bound to a competitive inhibitor implicates the catalytic cofactor in the chemical mechanism of strand scission by the ribozyme.
    • Klein D.J., and Ferre-D'Amare A.R. Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science 313 (2006) 1752-1756. X-ray crystal structure of the glmS ribozyme bound to a competitive inhibitor implicates the catalytic cofactor in the chemical mechanism of strand scission by the ribozyme.
    • (2006) Science , vol.313 , pp. 1752-1756
    • Klein, D.J.1    Ferre-D'Amare, A.R.2
  • 45
    • 33846279049 scopus 로고    scopus 로고
    • Structural investigation of the GlmS ribozyme bound to its catalytic cofactor
    • Structure of the glmS ribozyme bound to the GlcN6P activator and biochemical data on cofactor activation implicate GlcN6P as a general acid in ribozyme catalysis.
    • 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. Structure of the glmS ribozyme bound to the GlcN6P activator and biochemical data on cofactor activation implicate GlcN6P as a general acid in ribozyme catalysis.
    • (2007) Chem Biol , vol.14 , pp. 97-105
    • Cochrane, J.C.1    Lipchock, S.V.2    Strobel, S.A.3
  • 46
    • 33749354360 scopus 로고    scopus 로고
    • Structure of the 70S ribosome complexed with mRNA and tRNA
    • Selmer M., et al. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313 (2006) 1935-1942
    • (2006) Science , vol.313 , pp. 1935-1942
    • Selmer, M.1
  • 47
    • 27644598282 scopus 로고    scopus 로고
    • A protein component at the heart of an RNA machine: the importance of protein L27 for the function of the bacterial ribosome
    • Maguire B., Beniaminov A., Ramu H., Mankin A., and Zimmermann R. A protein component at the heart of an RNA machine: the importance of protein L27 for the function of the bacterial ribosome. Mol Cell 20 (2005) 427-435
    • (2005) Mol Cell , vol.20 , pp. 427-435
    • Maguire, B.1    Beniaminov, A.2    Ramu, H.3    Mankin, A.4    Zimmermann, R.5


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