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Volumn 15, Issue 3 SPEC. ISS., 2005, Pages 313-323

Structure, folding and mechanisms of ribozymes

Author keywords

[No Author keywords available]

Indexed keywords

BETA GLOBIN; PEPTIDYLTRANSFERASE; RIBONUCLEASE P; RIBOZYME;

EID: 20444502087     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2005.05.002     Document Type: Review
Times cited : (134)

References (89)
  • 1
    • 0041597294 scopus 로고
    • The evolution of the genetic code
    • New York: Harper & Row;
    • Woese C: The evolution of the genetic code. In The Genetic Code. New York: Harper & Row; 1967:179-195.
    • (1967) The Genetic Code , pp. 179-195
    • Woese, C.1
  • 2
    • 0014378880 scopus 로고
    • The origin of the genetic code
    • F.H.C. Crick The origin of the genetic code J Mol Biol 38 1968 367 379
    • (1968) J Mol Biol , vol.38 , pp. 367-379
    • Crick, F.H.C.1
  • 3
    • 0029147392 scopus 로고
    • Structurally complex and highly active RNA ligases derived from random RNA sequences
    • E.H. Ekland, J.W. Szostak, and D.P. Bartel Structurally complex and highly active RNA ligases derived from random RNA sequences Science 269 1995 364 370
    • (1995) Science , vol.269 , pp. 364-370
    • Ekland, E.H.1    Szostak, J.W.2    Bartel, D.P.3
  • 4
    • 0032542574 scopus 로고    scopus 로고
    • Structural and kinetic characterisation of an acyl-transferase ribozyme
    • H. Suga, P.A. Lohse, and J.W. Szostak Structural and kinetic characterisation of an acyl-transferase ribozyme J Am Chem Soc 120 1998 1151 1156
    • (1998) J Am Chem Soc , vol.120 , pp. 1151-1156
    • Suga, H.1    Lohse, P.A.2    Szostak, J.W.3
  • 5
    • 0032541654 scopus 로고    scopus 로고
    • RNA-catalysed nucleotide synthesis
    • P.J. Unrau, and D.P. Bartel RNA-catalysed nucleotide synthesis Nature 395 1998 260 263
    • (1998) Nature , vol.395 , pp. 260-263
    • Unrau, P.J.1    Bartel, D.P.2
  • 6
    • 0035906978 scopus 로고    scopus 로고
    • RNA-catalyzed RNA polymerization: Accurate and general RNA-templated primer extension
    • W.K. Johnston, P.J. Unrau, M.S. Lawrence, M.E. Glasner, and D.P. Bartel RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension Science 292 2001 1319 1325
    • (2001) Science , vol.292 , pp. 1319-1325
    • Johnston, W.K.1    Unrau, P.J.2    Lawrence, M.S.3    Glasner, M.E.4    Bartel, D.P.5
  • 7
    • 0037062978 scopus 로고    scopus 로고
    • The antiquity of RNA-based evolution
    • G.F. Joyce The antiquity of RNA-based evolution Nature 418 2002 214 221
    • (2002) Nature , vol.418 , pp. 214-221
    • Joyce, G.F.1
  • 8
    • 0030963855 scopus 로고    scopus 로고
    • RNA-catalysed carbon-carbon bond formation
    • T.M. Tarasow, S.L. Tarasow, and B.E. Eaton RNA-catalysed carbon-carbon bond formation Nature 389 1997 54 57
    • (1997) Nature , vol.389 , pp. 54-57
    • Tarasow, T.M.1    Tarasow, S.L.2    Eaton, B.E.3
  • 9
    • 0033102314 scopus 로고    scopus 로고
    • A small catalytic RNA motif with Diels-Alderase activity
    • B. Seelig, and A. Jäschke A small catalytic RNA motif with Diels-Alderase activity Chem Biol 6 1999 167 176
    • (1999) Chem Biol , vol.6 , pp. 167-176
    • Seelig, B.1    Jäschke, A.2
  • 10
    • 4644305780 scopus 로고    scopus 로고
    • Architecture of a Diels-Alderase ribozyme with a preformed catalytic pocket
    • S. Keiper, D. Bebenroth, B. Seelig, E. Westhof, and A. Jäschke Architecture of a Diels-Alderase ribozyme with a preformed catalytic pocket Chem Biol 11 2004 1217 1227
    • (2004) Chem Biol , vol.11 , pp. 1217-1227
    • Keiper, S.1    Bebenroth, D.2    Seelig, B.3    Westhof, E.4    Jäschke, A.5
  • 12
    • 0032214088 scopus 로고    scopus 로고
    • A novel allosterically trans-activated ribozyme, the maxizyme, with exceptional specificity in vitro and in vivo
    • T. Kuwabara, M. Warashina, T. Tanabe, K. Tani, S. Asano, and K. Taira A novel allosterically trans-activated ribozyme, the maxizyme, with exceptional specificity in vitro and in vivo Mol Cell 2 1998 617 627
    • (1998) Mol Cell , vol.2 , pp. 617-627
    • Kuwabara, T.1    Warashina, M.2    Tanabe, T.3    Tani, K.4    Asano, S.5    Taira, K.6
  • 13
    • 0032955410 scopus 로고    scopus 로고
    • In vitro selection of an allosteric ribozyme that transduces analytes to amplicons
    • M.P. Robertson, and A.D. Ellington In vitro selection of an allosteric ribozyme that transduces analytes to amplicons Nat Biotechnol 17 1999 62 66
    • (1999) Nat Biotechnol , vol.17 , pp. 62-66
    • Robertson, M.P.1    Ellington, A.D.2
  • 14
    • 0033565475 scopus 로고    scopus 로고
    • Design of allosteric hammerhead ribozymes activated by ligand-induced structure stabilization
    • G.A. Soukup, and R.R. Breaker Design of allosteric hammerhead ribozymes activated by ligand-induced structure stabilization Structure Fold Des 7 1999 783 791
    • (1999) Structure Fold des , vol.7 , pp. 783-791
    • Soukup, G.A.1    Breaker, R.R.2
  • 15
    • 4344633206 scopus 로고    scopus 로고
    • Deprotonation stimulates productive folding in allosteric TRAP hammerhead ribozymes
    • V. Saksmerprome, and D.H. Burke Deprotonation stimulates productive folding in allosteric TRAP hammerhead ribozymes J Mol Biol 341 2004 685 694
    • (2004) J Mol Biol , vol.341 , pp. 685-694
    • Saksmerprome, V.1    Burke, D.H.2
  • 16
    • 0034649666 scopus 로고    scopus 로고
    • Metal-ion coordination by U6 small nuclear RNA contributes to catalysis in the spliceosome
    • S.-L Yean, G. Wuenschell, J. Termini, and R.-J Lin 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
  • 17
    • 0035909314 scopus 로고    scopus 로고
    • Splicing-related catalysis by protein-free snRNAs
    • S. Valadkhan, and J.L. Manley Splicing-related catalysis by protein-free snRNAs Nature 413 2001 701 707
    • (2001) Nature , vol.413 , pp. 701-707
    • Valadkhan, S.1    Manley, J.L.2
  • 18
    • 0038719932 scopus 로고    scopus 로고
    • Characterization of the catalytic activity of U2 and U6 snRNAs
    • S. Valadkhan, and J.L. Manley Characterization of the catalytic activity of U2 and U6 snRNAs RNA 9 2003 892 904
    • (2003) RNA , vol.9 , pp. 892-904
    • Valadkhan, S.1    Manley, J.L.2
  • 19
    • 0142075327 scopus 로고    scopus 로고
    • Genetic control by metabolite-binding riboswitches
    • W.C. Winkler, and R.R. Breaker Genetic control by metabolite-binding riboswitches ChemBioChem 4 2003 1024 1032
    • (2003) ChemBioChem , vol.4 , pp. 1024-1032
    • Winkler, W.C.1    Breaker, R.R.2
  • 22
    • 0037165996 scopus 로고    scopus 로고
    • Correlating structural dynamics and function in single ribozyme molecules
    • X.W. Zhuang, H.D. Kim, M.J.B. Pereira, H.P. Babcock, N.G. Walter, and S. Chu Correlating structural dynamics and function in single ribozyme molecules Science 296 2002 1473 1476
    • (2002) Science , vol.296 , pp. 1473-1476
    • Zhuang, X.W.1    Kim, H.D.2    Pereira, M.J.B.3    Babcock, H.P.4    Walter, N.G.5    Chu, S.6
  • 24
    • 0043009768 scopus 로고    scopus 로고
    • A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate
    • E. Tan, T.J. Wilson, M.K. Nahas, R.M. Clegg, D.M.J. Lilley, and T. Ha A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate Proc Natl Acad Sci USA 100 2003 9308 9313 A single-molecule FRET study showing that the four-way junction introduces an obligate intermediate in the folding of the hairpin ribozyme that increases the rate of ion-induced folding by a factor of 500.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 9308-9313
    • Tan, E.1    Wilson, T.J.2    Nahas, M.K.3    Clegg, R.M.4    Lilley, D.M.J.5    Ha, T.6
  • 25
    • 7544231457 scopus 로고    scopus 로고
    • Observation of internal cleavage and ligation reactions of a ribozyme
    • M.K. Nahas, T.J. Wilson, S. Hohng, K. Jarvie, D.M.J. Lilley, and T. Ha Observation of internal cleavage and ligation reactions of a ribozyme Nat Struct Mol Biol 11 2004 1107 1113 Direct measurement of the rates of cleavage and ligation reactions of the hairpin ribozyme using single-molecule FRET. Multiple cycles of cleavage/ligation can be observed, and rates measured free of uncertainties caused by undocking and product release.
    • (2004) Nat Struct Mol Biol , vol.11 , pp. 1107-1113
    • Nahas, M.K.1    Wilson, T.J.2    Hohng, S.3    Jarvie, K.4    Lilley, D.M.J.5    Ha, T.6
  • 27
    • 0030476765 scopus 로고    scopus 로고
    • Capturing the structure of a catalytic RNA intermediate: The hammerhead ribozyme
    • W.G. Scott, J.B. Murray, J.R.P. Arnold, B.L. Stoddard, and A. Klug Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme Science 274 1996 2065 2069
    • (1996) Science , vol.274 , pp. 2065-2069
    • Scott, W.G.1    Murray, J.B.2    Arnold, J.R.P.3    Stoddard, B.L.4    Klug, A.5
  • 28
    • 0034635350 scopus 로고    scopus 로고
    • Does a single metal ion bridge the A-9 and scissile phosphate groups in the catalytically active hammerhead ribozyme structure?
    • J.B. Murray, and W.G. Scott Does a single metal ion bridge the A-9 and scissile phosphate groups in the catalytically active hammerhead ribozyme structure? J Mol Biol 296 2000 33 41
    • (2000) J Mol Biol , vol.296 , pp. 33-41
    • Murray, J.B.1    Scott, W.G.2
  • 29
    • 0033860560 scopus 로고    scopus 로고
    • Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction
    • J.B. Murray, H. Szöke, A. Szöke, and W.G. Scott Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction Mol Cell 5 2000 279 287
    • (2000) Mol Cell , vol.5 , pp. 279-287
    • Murray, J.B.1    Szöke, H.2    Szöke, A.3    Scott, W.G.4
  • 30
    • 0036293201 scopus 로고    scopus 로고
    • A pH-dependent conformational change, rather than the chemical step, appears to be rate-limiting in the hammerhead ribozyme cleavage reaction
    • J.B. Murray, C.M. Dunham, and W.G. Scott A pH-dependent conformational change, rather than the chemical step, appears to be rate-limiting in the hammerhead ribozyme cleavage reaction J Mol Biol 315 2002 121 130
    • (2002) J Mol Biol , vol.315 , pp. 121-130
    • Murray, J.B.1    Dunham, C.M.2    Scott, W.G.3
  • 32
    • 0032497521 scopus 로고    scopus 로고
    • Crystal structure of a hepatitis delta virus ribozyme
    • A.R. Ferré-d'Amaré, K. Zhou, and J.A. Doudna Crystal structure of a hepatitis delta virus ribozyme Nature 395 1998 567 574
    • (1998) Nature , vol.395 , pp. 567-574
    • Ferré-D'Amaré, A.R.1    Zhou, K.2    Doudna, J.A.3
  • 33
    • 0035848837 scopus 로고    scopus 로고
    • Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis
    • P.B. Rupert, and A.R. Ferré-D'Amaré Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis Nature 410 2001 780 786
    • (2001) Nature , vol.410 , pp. 780-786
    • Rupert, P.B.1    Ferré-D'Amaré, A.R.2
  • 35
    • 2442641641 scopus 로고    scopus 로고
    • A conformational switch controls hepatitis delta virus ribozyme catalysis
    • A. Ke, K. Zhou, F. Ding, J.H. Cate, and J.A. Doudna A conformational switch controls hepatitis delta virus ribozyme catalysis Nature 429 2004 201 205 New crystal structures of the HDV ribozyme show a well-defined metal ion bound in the active site.
    • (2004) Nature , vol.429 , pp. 201-205
    • Ke, A.1    Zhou, K.2    Ding, F.3    Cate, J.H.4    Doudna, J.A.5
  • 36
    • 0032500731 scopus 로고    scopus 로고
    • A preorganised active site in the crystal structure of the Tetrahymena ribozyme
    • B.L. Golden, A.R. Gooding, E. Podell, and T.R. Cech A preorganised active site in the crystal structure of the Tetrahymena ribozyme Science 282 1998 259 264
    • (1998) Science , vol.282 , pp. 259-264
    • Golden, B.L.1    Gooding, A.R.2    Podell, E.3    Cech, T.R.4
  • 37
    • 8644229237 scopus 로고    scopus 로고
    • Structure of the Tetrahymena ribozyme; Base triple sandwich and metal ion at the active site
    • F. Guo, A.R. Gooding, and T.R. Cech Structure of the Tetrahymena ribozyme; base triple sandwich and metal ion at the active site Mol Cell 16 2004 351 362 The crystal structure of the Tetrahymena ribozyme at the stage before substrate binding.
    • (2004) Mol Cell , vol.16 , pp. 351-362
    • Guo, F.1    Gooding, A.R.2    Cech, T.R.3
  • 38
    • 3042848954 scopus 로고    scopus 로고
    • Crystal structure of a self-splicing group I intron with both exons
    • P.L. Adams, M.R. Stahley, J. Wang, and S.A. Strobel Crystal structure of a self-splicing group I intron with both exons Nature 430 2004 45 50 The crystal structure of the Azoarcus group I ribozyme with both exons, trapped at the stage preceding the second transesterification reaction that will join the exons. The 3′ hydroxyl of the 5′ exon fragment is positioned for in-line attack on the phosphate of the ΩG located at the 3′ end of the intron. Two metal ions flank the scissile phosphate, bound by several inner-sphere phosphate interactions.
    • (2004) Nature , vol.430 , pp. 45-50
    • Adams, P.L.1    Stahley, M.R.2    Wang, J.3    Strobel, S.A.4
  • 39
    • 11444263264 scopus 로고    scopus 로고
    • Crystal structure of a phage Twort group I ribozyme-product complex
    • B.L. Golden, H.D. Kim, and E. Chase Crystal structure of a phage Twort group I ribozyme-product complex Nat Struct Mol Biol 12 2005 82 89 The crystal structure of a relatively elaborated group I ribozyme from phage Twort.
    • (2005) Nat Struct Mol Biol , vol.12 , pp. 82-89
    • Golden, B.L.1    Kim, H.D.2    Chase, E.3
  • 40
    • 0025678737 scopus 로고
    • Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis
    • F. Michel, and E. Westhof Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis J Mol Biol 216 1990 585 610
    • (1990) J Mol Biol , vol.216 , pp. 585-610
    • Michel, F.1    Westhof, E.2
  • 41
    • 0030452773 scopus 로고    scopus 로고
    • New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: A complete 3D model of the Tetrahymena thermophila ribozyme
    • V. Lehnert, L. Jaeger, F. Michel, and E. Westhof 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 3 1996 993 1009
    • (1996) Chem Biol , vol.3 , pp. 993-1009
    • Lehnert, V.1    Jaeger, L.2    Michel, F.3    Westhof, E.4
  • 42
    • 0024427177 scopus 로고
    • The guanosine binding site of the Tetrahymena ribozyme
    • F. Michel, M. Hanna, R. Green, D.P. Bartel, and J.W. Szostak The guanosine binding site of the Tetrahymena ribozyme Nature 342 1989 391 395
    • (1989) Nature , vol.342 , pp. 391-395
    • Michel, F.1    Hanna, M.2    Green, R.3    Bartel, D.P.4    Szostak, J.W.5
  • 44
    • 0035340961 scopus 로고    scopus 로고
    • Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction
    • S. Shan, A.V. Kravchuk, J.A. Piccirilli, and D. Herschlag Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction Biochemistry 40 2001 5161 5171
    • (2001) Biochemistry , vol.40 , pp. 5161-5171
    • Shan, S.1    Kravchuk, A.V.2    Piccirilli, J.A.3    Herschlag, D.4
  • 45
    • 0037176844 scopus 로고    scopus 로고
    • Identification of an active site ligand for a group I ribozyme catalytic metal ion
    • A.A. Szewczak, A.B. Kosek, J.A. Piccirilli, and S.A. Strobel Identification of an active site ligand for a group I ribozyme catalytic metal ion Biochemistry 41 2002 2516 2525
    • (2002) Biochemistry , vol.41 , pp. 2516-2525
    • Szewczak, A.A.1    Kosek, A.B.2    Piccirilli, J.A.3    Strobel, S.A.4
  • 46
    • 0037434709 scopus 로고    scopus 로고
    • Crystal structure of the specificity domain of ribonuclease P
    • A.S. Krasilnikov, X. Yang, T. Pan, and A. Mondragon Crystal structure of the specificity domain of ribonuclease P Nature 421 2003 760 764 The crystal structure of the specificity domain of the P-RNA of RNaseP from B. subtilis.
    • (2003) Nature , vol.421 , pp. 760-764
    • Krasilnikov, A.S.1    Yang, X.2    Pan, T.3    Mondragon, A.4
  • 48
    • 0033600553 scopus 로고    scopus 로고
    • Tertiary structure stabilization promotes hairpin ribozyme ligation
    • M.J. Fedor Tertiary structure stabilization promotes hairpin ribozyme ligation Biochemistry 38 1999 11040 11050
    • (1999) Biochemistry , vol.38 , pp. 11040-11050
    • Fedor, M.J.1
  • 50
    • 0033575087 scopus 로고    scopus 로고
    • Kinetics of RNA degradation by specific base catalysis of transesterification involving the 2′-hydroxyl group
    • Y. Li, and R.R. Breaker Kinetics of RNA degradation by specific base catalysis of transesterification involving the 2′-hydroxyl group J Am Chem Soc 121 1999 5364 5372
    • (1999) J Am Chem Soc , vol.121 , pp. 5364-5372
    • Li, Y.1    Breaker, R.R.2
  • 52
    • 0041702195 scopus 로고    scopus 로고
    • Ribozyme speed limits
    • G.M. Emilsson, S. Nakamura, A. Roth, and R.R. Breaker Ribozyme speed limits RNA 9 2003 907 918 A thoughtful analysis of the mechanisms and rate enhancements possible for nucleolytic ribozymes.
    • (2003) RNA , vol.9 , pp. 907-918
    • Emilsson, G.M.1    Nakamura, S.2    Roth, A.3    Breaker, R.R.4
  • 56
    • 0025335881 scopus 로고
    • Two autolytic processing reactions of a satellite RNA proceed with inversion of configuration
    • H. van Tol, J.M. Buzayan, P.A. Feldstein, F. Eckstein, and G. Bruening Two autolytic processing reactions of a satellite RNA proceed with inversion of configuration Nucleic Acids Res 18 1990 1971 1975
    • (1990) Nucleic Acids Res , vol.18 , pp. 1971-1975
    • Van Tol, H.1    Buzayan, J.M.2    Feldstein, P.A.3    Eckstein, F.4    Bruening, G.5
  • 58
    • 0026102040 scopus 로고
    • Configurationally defined phosphorothioate-containing oligoribonucleotides in the study of the mechanism of cleavage of hammerhead ribozymes
    • G. Slim, and M.J. Gait Configurationally defined phosphorothioate- containing oligoribonucleotides in the study of the mechanism of cleavage of hammerhead ribozymes Nucleic Acids Res 19 1991 1183 1188
    • (1991) Nucleic Acids Res , vol.19 , pp. 1183-1188
    • Slim, G.1    Gait, M.J.2
  • 59
    • 0001055719 scopus 로고    scopus 로고
    • Kinetics and mechanisms for the cleavage and isomerization of the phosphodiester bonds of RNA by Brönsted acids and bases
    • M. Oivanen, S. Kuusela, and H. Lonnberg Kinetics and mechanisms for the cleavage and isomerization of the phosphodiester bonds of RNA by Brönsted acids and bases Chem Rev 98 1998 961 990
    • (1998) Chem Rev , vol.98 , pp. 961-990
    • Oivanen, M.1    Kuusela, S.2    Lonnberg, H.3
  • 60
    • 0032831634 scopus 로고    scopus 로고
    • Relationship between internucleotide linkage geometry and the stability of RNA
    • G.A. Soukup, and R.R. Breaker Relationship between internucleotide linkage geometry and the stability of RNA RNA 5 1999 1308 1325
    • (1999) RNA , vol.5 , pp. 1308-1325
    • Soukup, G.A.1    Breaker, R.R.2
  • 61
    • 0030747007 scopus 로고    scopus 로고
    • Unusual dynamics and pKa shift at the active site of a lead-dependent ribozyme
    • P. Legault, and A. Pardi Unusual dynamics and pKa shift at the active site of a lead-dependent ribozyme J Am Chem Soc 119 1997 6621 6628
    • (1997) J Am Chem Soc , vol.119 , pp. 6621-6628
    • Legault, P.1    Pardi, A.2
  • 62
    • 0037418547 scopus 로고    scopus 로고
    • Mechanistic considerations for general acid-base catalysis by RNA: Revisiting the mechanism of the hairpin ribozyme
    • P.C. Bevilacqua Mechanistic considerations for general acid-base catalysis by RNA: revisiting the mechanism of the hairpin ribozyme Biochemistry 42 2003 2259 2265 A valuable discussion of how pH can affect the reaction rate when ribozymes employ general acid-base catalysis.
    • (2003) Biochemistry , vol.42 , pp. 2259-2265
    • Bevilacqua, P.C.1
  • 64
    • 0035916297 scopus 로고    scopus 로고
    • Importance of specific nucleotides in the folding of the natural form of the hairpin ribozyme
    • T.J. Wilson, Z.-Y Zhao, K. Maxwell, L. Kontogiannis, and D.M.J. Lilley Importance of specific nucleotides in the folding of the natural form of the hairpin ribozyme Biochemistry 40 2001 2291 2302
    • (2001) Biochemistry , vol.40 , pp. 2291-2302
    • Wilson, T.J.1    Zhao, Z.-Y.2    Maxwell, K.3    Kontogiannis, L.4    Lilley, D.M.J.5
  • 65
    • 2942577491 scopus 로고    scopus 로고
    • Role of an active site guanine in hairpin ribozyme catalysis probed by exogenous nucleobase rescue
    • Y.I. Kuzmin, C.P. Da Costa, and M.J. Fedor Role of an active site guanine in hairpin ribozyme catalysis probed by exogenous nucleobase rescue J Mol Biol 340 2004 233 251 The authors illustrate the pH dependence of the reaction rate of the hairpin ribozyme containing modified nucleotides such as 2-aminopurine and 2,6-diaminopurine at position 8 (normally a guanine).
    • (2004) J Mol Biol , vol.340 , pp. 233-251
    • Kuzmin, Y.I.1    Da Costa, C.P.2    Fedor, M.J.3
  • 66
    • 0036237379 scopus 로고    scopus 로고
    • Rescue of an abasic hairpin ribozyme by cationic nucleobases. Evidence for a novel mechanism of RNA catalysis
    • L.L. Lebruska, I. Kuzmine, and M.J. Fedor Rescue of an abasic hairpin ribozyme by cationic nucleobases. Evidence for a novel mechanism of RNA catalysis Chem Biol 9 2002 465 473
    • (2002) Chem Biol , vol.9 , pp. 465-473
    • Lebruska, L.L.1    Kuzmine, I.2    Fedor, M.J.3
  • 67
    • 0031194873 scopus 로고    scopus 로고
    • A unique mechanism for RNA catalysis: The role of metal cofactors in hairpin ribozyme cleavage
    • A. Hampel, and J.A. Cowan A unique mechanism for RNA catalysis: the role of metal cofactors in hairpin ribozyme cleavage Chem Biol 4 1997 513 517
    • (1997) Chem Biol , vol.4 , pp. 513-517
    • Hampel, A.1    Cowan, J.A.2
  • 68
    • 0031215134 scopus 로고    scopus 로고
    • An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis
    • S. Nesbitt, L.A. Hegg, and M.J. Fedor An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis Chem Biol 4 1997 619 630
    • (1997) Chem Biol , vol.4 , pp. 619-630
    • Nesbitt, S.1    Hegg, L.A.2    Fedor, M.J.3
  • 69
    • 0030967825 scopus 로고    scopus 로고
    • Metal ions play a passive role in the hairpin ribozyme catalysed reaction
    • K.J. Young, F. Gill, and J.A. Grasby Metal ions play a passive role in the hairpin ribozyme catalysed reaction Nucleic Acids Res 25 1997 3760 3766
    • (1997) Nucleic Acids Res , vol.25 , pp. 3760-3766
    • Young, K.J.1    Gill, F.2    Grasby, J.A.3
  • 70
    • 0032192761 scopus 로고    scopus 로고
    • The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone
    • J.B. Murray, A.A. Seyhan, N.G. Walter, J.M. Burke, and W.G. Scott 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
  • 71
    • 0033215448 scopus 로고    scopus 로고
    • Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme
    • A.T. Perrotta, I. Shih, and M.D. Been 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
  • 72
    • 0034712097 scopus 로고    scopus 로고
    • General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme
    • S. Nakano, D.M. Chadalavada, and P.C. Bevilacqua 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
  • 74
    • 0034637161 scopus 로고    scopus 로고
    • The structural basis of ribosome activity in peptide bond synthesis
    • P. Nissen, J. Hansen, N. Ban, P.B. Moore, and T.A. Steitz 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.B.4    Steitz, T.A.5
  • 75
    • 0026639881 scopus 로고
    • Unusual resistance of peptidyl transferase to protein extraction procedures
    • H.F. Noller, V. Hoffarth, and L. Zimniak Unusual resistance of peptidyl transferase to protein extraction procedures Science 256 1992 1416 1419
    • (1992) Science , vol.256 , pp. 1416-1419
    • Noller, H.F.1    Hoffarth, V.2    Zimniak, L.3
  • 77
    • 0035942753 scopus 로고    scopus 로고
    • Ribosomal peptidyl transferase can withstand mutations at the putative catalytic nucleotide
    • N. Polacek, M. Gaynor, A. Yassin, and A.S. Mankin 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
  • 78
    • 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
    • E.M. Youngman, J.L. Brunelle, A.B. Kochaniak, and R. Green 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 Mutation of an inner shell of nucleotides around the peptidyl transferase centre of the ribosome fails to impair the rate of peptide bond formation, but leads to substantial defects in peptide release.
    • (2004) Cell , vol.117 , pp. 589-599
    • Youngman, E.M.1    Brunelle, J.L.2    Kochaniak, A.B.3    Green, R.4
  • 79
    • 0036671344 scopus 로고    scopus 로고
    • Important contribution to catalysis of peptide bond formation by a single ionizing group within the ribosome
    • V.I. Katunin, G.W. Muth, S.A. Strobel, W. Wintermeyer, and M.V. Rodnina Important contribution to catalysis of peptide bond formation by a single ionizing group within the ribosome Mol Cell 10 2002 339 346
    • (2002) Mol Cell , vol.10 , pp. 339-346
    • Katunin, V.I.1    Muth, G.W.2    Strobel, S.A.3    Wintermeyer, W.4    Rodnina, M.V.5
  • 80
    • 0038359320 scopus 로고    scopus 로고
    • The G2447A mutation does not affect ionization of a ribosomal group taking part in peptide bond formation
    • M. Beringer, S. Adio, W. Wintermeyer, and M. Rodnina The G2447A mutation does not affect ionization of a ribosomal group taking part in peptide bond formation RNA 9 2003 919 922 The G2447A mutation leads to a tenfold lower rate compared to wild-type, but does not alter the pH dependence.
    • (2003) RNA , vol.9 , pp. 919-922
    • Beringer, M.1    Adio, S.2    Wintermeyer, W.3    Rodnina, M.4
  • 82
    • 7544220590 scopus 로고    scopus 로고
    • Substrate-assisted catalysis of peptide bond formation by the ribosome
    • 6-fold reduction in rate results from changing A76 of the tRNA bound to the P-site to 2′ deoxy or fluoro. It is suggested that the 2′ oxygen serves as general base to remove a proton from the nucleophilic amino group.
    • (2004) Nat Struct Mol Biol , vol.11 , pp. 1101-1106
    • Weinger, J.S.1    Parnell, K.M.2    Dorner, S.3    Green, R.4    Strobel, S.A.5
  • 83
    • 0042821577 scopus 로고    scopus 로고
    • Ribozymes - A snip too far?
    • D.M.J. Lilley Ribozymes - a snip too far? Nat Struct Biol 10 2003 672 673
    • (2003) Nat Struct Biol , vol.10 , pp. 672-673
    • Lilley, D.M.J.1
  • 85
    • 0034545071 scopus 로고    scopus 로고
    • The folding of the hairpin ribozyme: Dependence on the loops and the junction
    • Z.-Y Zhao, T.J. Wilson, K. Maxwell, and D.M.J. Lilley The folding of the hairpin ribozyme: dependence on the loops and the junction RNA 6 2000 1833 1846
    • (2000) RNA , vol.6 , pp. 1833-1846
    • Zhao, Z.-Y.1    Wilson, T.J.2    Maxwell, K.3    Lilley, D.M.J.4
  • 86
    • 0034814785 scopus 로고    scopus 로고
    • A covalent crosslink converts the hammerhead ribozyme from a ribonuclease to an RNA ligase
    • T.K. Stage-Zimmermann, and O.C. Uhlenbeck A covalent crosslink converts the hammerhead ribozyme from a ribonuclease to an RNA ligase Nat Struct Biol 8 2001 863 867
    • (2001) Nat Struct Biol , vol.8 , pp. 863-867
    • Stage-Zimmermann, T.K.1    Uhlenbeck, O.C.2
  • 87
    • 0037188361 scopus 로고    scopus 로고
    • Internal equilibrium of the hammerhead ribozyme is altered by the length of certain covalent cross-links
    • K.F. Blount, and O.C. Uhlenbeck Internal equilibrium of the hammerhead ribozyme is altered by the length of certain covalent cross-links Biochemistry 41 2002 6834 6841
    • (2002) Biochemistry , vol.41 , pp. 6834-6841
    • Blount, K.F.1    Uhlenbeck, O.C.2
  • 88
    • 0033607198 scopus 로고    scopus 로고
    • Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate
    • S. Wang, K. Karbstein, A. Peracchi, L. Beigelman, and D. Herschlag Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate Biochemistry 38 1999 14363 14378
    • (1999) Biochemistry , vol.38 , pp. 14363-14378
    • Wang, S.1    Karbstein, K.2    Peracchi, A.3    Beigelman, L.4    Herschlag, D.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.