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Volumn 17, Issue 23, 1998, Pages 7105-7117

A map of the binding site for catalytic domain 5 in the core of a group II intron ribozyme

Author keywords

Catalysis; Folding; RNA; Splicing; Tertiary structure

Indexed keywords

DIMETHYL SULFATE; RIBOZYME; RNA;

EID: 0032401749     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/17.23.7105     Document Type: Article
Times cited : (27)

References (45)
  • 1
    • 0031588542 scopus 로고    scopus 로고
    • Remarkable morphological variability of a common RNA folding motif: The GNRA tetraloop-receptor interaction
    • Abramovitz, D.L. and Pyle, A.M. (1997) Remarkable morphological variability of a common RNA folding motif: the GNRA tetraloop-receptor interaction. J. Mol. Biol., 266, 493-506.
    • (1997) J. Mol. Biol. , vol.266 , pp. 493-506
    • Abramovitz, D.L.1    Pyle, A.M.2
  • 2
    • 0029670279 scopus 로고    scopus 로고
    • Catalytic role of 2′-hydroxyl groups within a group II intron active site
    • Abramovitz, D.L., Friedman, R.A. and Pyle, A.M. (1996) Catalytic role of 2′-hydroxyl groups within a group II intron active site. Science, 271, 1410-1413.
    • (1996) Science , vol.271 , pp. 1410-1413
    • Abramovitz, D.L.1    Friedman, R.A.2    Pyle, A.M.3
  • 3
    • 0027930184 scopus 로고
    • A kinetic mechanism for cleavage of pre-tRNA Asp catalyzed by the RNA component of Bacillus subtilis Ribonuclease P
    • Beebe, J.A. and Fierke, C.A. (1994) A kinetic mechanism for cleavage of pre-tRNA Asp catalyzed by the RNA component of Bacillus subtilis Ribonuclease P. Biochemistry, 33, 10294-10304.
    • (1994) Biochemistry , vol.33 , pp. 10294-10304
    • Beebe, J.A.1    Fierke, C.A.2
  • 4
    • 0032404048 scopus 로고    scopus 로고
    • Defining the functional groups. core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: A NAIM analysis
    • Boudvillain, M. and Pyle, A.M. (1998) Defining the functional groups. core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: a NAIM analysis. EMBO J., 17, 7091-7104.
    • (1998) EMBO J. , vol.17 , pp. 7091-7104
    • Boudvillain, M.1    Pyle, A.M.2
  • 6
    • 0028569768 scopus 로고
    • Catalytic site components common to both splicing steps of a group II intron
    • Chanfreau, G. and Jacquier, A. (1994) Catalytic site components common to both splicing steps of a group II intron. Science, 266, 1383-1387.
    • (1994) Science , vol.266 , pp. 1383-1387
    • Chanfreau, G.1    Jacquier, A.2
  • 7
    • 0030015953 scopus 로고    scopus 로고
    • An RNA conformational change between the two chemical steps of group II self-splicing
    • Chanfreau, G. and Jacquier, A. (1996) An RNA conformational change between the two chemical steps of group II self-splicing. EMBO J., 15, 3466-3476.
    • (1996) EMBO J. , vol.15 , pp. 3466-3476
    • Chanfreau, G.1    Jacquier, A.2
  • 8
    • 0024811039 scopus 로고
    • Modification interference analysis of reactions using RNA substrates
    • Conway, L. and Wickens, M. (1989) Modification interference analysis of reactions using RNA substrates. Methods Enzymol., 180, 369-379.
    • (1989) Methods Enzymol. , vol.180 , pp. 369-379
    • Conway, L.1    Wickens, M.2
  • 9
    • 0028921811 scopus 로고
    • Frequent use of the same tertiary motif by self-folding RNAs
    • Costa, M. and Michel, F. (1995) Frequent use of the same tertiary motif by self-folding RNAs. EMBO J., 14, 1276-1285.
    • (1995) EMBO J. , vol.14 , pp. 1276-1285
    • Costa, M.1    Michel, F.2
  • 10
    • 0031552355 scopus 로고    scopus 로고
    • Multiple tertiary interactions involving domain II of group II self-splicing introns
    • Costa, M., Deme, E., Jacquier, A. and Michel, F. (1997) Multiple tertiary interactions involving domain II of group II self-splicing introns. J. Mol. Biol., 267, 520-536.
    • (1997) J. Mol. Biol. , vol.267 , pp. 520-536
    • Costa, M.1    Deme, E.2    Jacquier, A.3    Michel, F.4
  • 11
    • 0029258956 scopus 로고
    • Self-assembly of a group I intron active site from its component tertiary structural domains
    • Doudna, J.A. and Cech, T.R. (1995) Self-assembly of a group I intron active site from its component tertiary structural domains. RNA, 1, 36-45.
    • (1995) RNA , vol.1 , pp. 36-45
    • Doudna, J.A.1    Cech, T.R.2
  • 12
    • 0027285186 scopus 로고
    • Kinetic analysis of the 5′-splice junction hydrolysis of a Group II intron promoted by Domain 5
    • Franzen, J.S., Zhang, M. and Peebles, C.L. (1993) Kinetic analysis of the 5′-splice junction hydrolysis of a Group II intron promoted by Domain 5. Nucleic Acids Res., 21, 627-634.
    • (1993) Nucleic Acids Res. , vol.21 , pp. 627-634
    • Franzen, J.S.1    Zhang, M.2    Peebles, C.L.3
  • 13
    • 0029410699 scopus 로고
    • Group II intron ribozymes that cleave DNA and RNA linkages with similar efficiency and lack contacts with substrate 2′-hydroxyl groups
    • Griffin, E.A., Qin, Z.-F., Michels, W.A. and Pyle, A.M. (1995) Group II intron ribozymes that cleave DNA and RNA linkages with similar efficiency and lack contacts with substrate 2′-hydroxyl groups. Chem. Biol., 2, 761-770.
    • (1995) Chem. Biol. , vol.2 , pp. 761-770
    • Griffin, E.A.1    Qin, Z.-F.2    Michels, W.A.3    Pyle, A.M.4
  • 14
    • 0027491314 scopus 로고
    • The phylogenetically predicted base-pairing interaction between α and α′ is required for group II splicing in vitro
    • Harris-Kerr, C.L., Zhang, M. and Peebles, C.L. (1993) The phylogenetically predicted base-pairing interaction between α and α′ is required for group II splicing in vitro. Proc. Natl Acad. Sci. USA, 90, 10658-10662.
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 10658-10662
    • Harris-Kerr, C.L.1    Zhang, M.2    Peebles, C.L.3
  • 15
    • 0021991295 scopus 로고
    • Secondary structure of the circular form of the Tetrahymena rRNA intervening sequence: A technique for RNA structure analysis using chemical probes and reverse transcriptase
    • Inouye, T. and Cech, T.R. (1985) Secondary structure of the circular form of the Tetrahymena rRNA intervening sequence: A technique for RNA structure analysis using chemical probes and reverse transcriptase. Proc. Natl Acad. Sci. USA, 82, 648-652.
    • (1985) Proc. Natl Acad. Sci. USA , vol.82 , pp. 648-652
    • Inouye, T.1    Cech, T.R.2
  • 16
    • 0023643081 scopus 로고
    • Multiple exon-binding sites in class II self-splicing introns
    • Jacquier, A. and Michel, F. (1987) Multiple exon-binding sites in class II self-splicing introns. Cell, 50, 17-29.
    • (1987) Cell , vol.50 , pp. 17-29
    • Jacquier, A.1    Michel, F.2
  • 17
    • 0025344901 scopus 로고
    • Base-pairing interactions involving the 5′- And 3′-terminal nucleotides of group II self-splicing introns
    • Jacquier, A. and Michel, F. (1990) Base-pairing interactions involving the 5′-and 3′-terminal nucleotides of group II self-splicing introns. J. Mol. Biol., 213, 437-447.
    • (1990) J. Mol. Biol. , vol.213 , pp. 437-447
    • Jacquier, A.1    Michel, F.2
  • 18
    • 0024022167 scopus 로고
    • Group II Intron Domain 5 facilitates a trans-splicing reaction
    • Jarrell, K.A., Dietrich, R.C. and Perlman, P.S. (1988) Group II Intron Domain 5 facilitates a trans-splicing reaction. Mol. Cell. Biol., 8, 2361-2366.
    • (1988) Mol. Cell. Biol. , vol.8 , pp. 2361-2366
    • Jarrell, K.A.1    Dietrich, R.C.2    Perlman, P.S.3
  • 19
    • 0343742528 scopus 로고    scopus 로고
    • Identification of structural elements critical for inter-domain interactions in a group II self-splicing intron
    • Jestin, J.-L., Deme, E. and Jacquier, A. (1997) Identification of structural elements critical for inter-domain interactions in a group II self-splicing intron. EMBO J., 16, 2945-2954.
    • (1997) EMBO J. , vol.16 , pp. 2945-2954
    • Jestin, J.-L.1    Deme, E.2    Jacquier, A.3
  • 20
    • 0026695012 scopus 로고
    • Group II introns deleted for multiple substructures retain self-splicing activity
    • Koch, J.L., Boulanger, S.C., Dib-Hajj, S., Hebbar, S.K. and Perlman, P.S. (1992) Group II introns deleted for multiple substructures retain self-splicing activity. Mol. Cell. Biol., 12, 1950-1958.
    • (1992) Mol. Cell. Biol. , vol.12 , pp. 1950-1958
    • Koch, J.L.1    Boulanger, S.C.2    Dib-Hajj, S.3    Hebbar, S.K.4    Perlman, P.S.5
  • 22
    • 0025888264 scopus 로고
    • Efficient site-directed mutagenesis using uracil-containing DNA
    • Kunkel, T.A., Bebenek, K. and McClary, J. (1991) Efficient site-directed mutagenesis using uracil-containing DNA. Methods Enzymol., 204, 125-139.
    • (1991) Methods Enzymol. , vol.204 , pp. 125-139
    • Kunkel, T.A.1    Bebenek, K.2    McClary, J.3
  • 23
    • 0025165413 scopus 로고
    • Structural analysis of a group II intron by chemical modifications and minimal energy calculations
    • Kwakman, J.H., Konings, D.A., Hogeweg, P., Pel, H.J. and Grivell, L.A. (1990) Structural analysis of a group II intron by chemical modifications and minimal energy calculations. J. Biomol. Struct. Dyn., 8, 413-430.
    • (1990) J. Biomol. Struct. Dyn. , vol.8 , pp. 413-430
    • Kwakman, J.H.1    Konings, D.A.2    Hogeweg, P.3    Pel, H.J.4    Grivell, L.A.5
  • 24
    • 0029001288 scopus 로고
    • Bent helix formation between RNA hairpins with complementary loops
    • Marino, J.P., Gregorian, R.S., Csankovszki, G. and Crothers, D.M. (1995) Bent helix formation between RNA hairpins with complementary loops. Science, 268, 1448-1454.
    • (1995) Science , vol.268 , pp. 1448-1454
    • Marino, J.P.1    Gregorian, R.S.2    Csankovszki, G.3    Crothers, D.M.4
  • 25
    • 0032546728 scopus 로고    scopus 로고
    • Derivation of the three-dimensional architecture of bacterial Ribonuclease P RNAs from comparative sequence analysis
    • Massire, C., Jaeger, L. and Westhof, E. (1998) Derivation of the three-dimensional architecture of bacterial Ribonuclease P RNAs from comparative sequence analysis. J. Mol. Biol., 279, 773-793.
    • (1998) J. Mol. Biol. , vol.279 , pp. 773-793
    • Massire, C.1    Jaeger, L.2    Westhof, E.3
  • 26
    • 0029066770 scopus 로고
    • Structure and activities of group II introns
    • Michel, F. and Ferat, J.-L. (1995) Structure and activities of group II introns. Annu. Rev. Biochem., 64, 435-461.
    • (1995) Annu. Rev. Biochem. , vol.64 , pp. 435-461
    • Michel, F.1    Ferat, J.-L.2
  • 27
    • 0024428420 scopus 로고
    • Comparative and functional anatomy of group II catalytic introns - A review
    • Michel, F., Umesono, K. and Ozeki, H. (1989) Comparative and functional anatomy of group II catalytic introns - a review. Gene, 82, 5-30.
    • (1989) Gene , vol.82 , pp. 5-30
    • Michel, F.1    Umesono, K.2    Ozeki, H.3
  • 28
    • 0028904152 scopus 로고
    • Conversion of a group II intron into a new multiple-turnover ribozyme that selectively cleaves oligonucleotides: Elucidation of reaction mechanism and structure/ function relationships
    • Michels, W.J. and Pyle, A.M. (1995) Conversion of a group II intron into a new multiple-turnover ribozyme that selectively cleaves oligonucleotides: elucidation of reaction mechanism and structure/ function relationships. Biochemistry, 34, 2965-2977.
    • (1995) Biochemistry , vol.34 , pp. 2965-2977
    • Michels, W.J.1    Pyle, A.M.2
  • 29
    • 0022470564 scopus 로고
    • Rapid chemical probing of conformation in 16S ribosomal subunits using primer extension
    • Moazed, D., Stern, S. and Noller, H.F. (1986) Rapid chemical probing of conformation in 16S ribosomal subunits using primer extension. J. Mol. Biol., 187, 399-416.
    • (1986) J. Mol. Biol. , vol.187 , pp. 399-416
    • Moazed, D.1    Stern, S.2    Noller, H.F.3
  • 30
    • 0027173193 scopus 로고
    • An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme
    • Murphy, F.L. and Cech, T.R. (1993) An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme. Biochemistry, 32, 5291-5300.
    • (1993) Biochemistry , vol.32 , pp. 5291-5300
    • Murphy, F.L.1    Cech, T.R.2
  • 31
    • 0028990228 scopus 로고
    • Identification of a catalytically critical trinucleotide in Domain 5 of a group II intron
    • Peebles, C.L., Zhang, M., Perlman, P.S. and Franzen, J.F. (1995) Identification of a catalytically critical trinucleotide in Domain 5 of a group II intron. Proc. Natl Acad. Sci. USA, 92, 4422-4426.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 4422-4426
    • Peebles, C.L.1    Zhang, M.2    Perlman, P.S.3    Franzen, J.F.4
  • 32
    • 0029382528 scopus 로고
    • A UV-induced Mg2+-dependent cross-link traps an active form of Domain 3 of a self-splicing group II intron
    • Podar, M., Dib-Hajj, S. and Perlman, P.S. (1995a) A UV-induced Mg2+-dependent cross-link traps an active form of Domain 3 of a self-splicing group II intron. RNA, 1, 828-840.
    • (1995) RNA , vol.1 , pp. 828-840
    • Podar, M.1    Dib-Hajj, S.2    Perlman, P.S.3
  • 33
    • 0029061712 scopus 로고
    • Stereochemical selectivity of group II intron splicing, reverse-splicing and hydrolysis reactions
    • Podar, M., Perlman, P.S. and Padgett, R.A. (1995b) Stereochemical selectivity of group II intron splicing, reverse-splicing and hydrolysis reactions. Mol. Cell. Biol., 15, 4466-4478.
    • (1995) Mol. Cell. Biol. , vol.15 , pp. 4466-4478
    • Podar, M.1    Perlman, P.S.2    Padgett, R.A.3
  • 34
    • 0031939815 scopus 로고    scopus 로고
    • Domain 5 binds near a highly-conserved dinucleotide in the joiner linking domains 2 and 3 of a group II intron
    • Podar, M., Zhou, J., Zhang, M., Franzen, J.S., Perlman, P.S. and Peebles, C.L. (1998) Domain 5 binds near a highly-conserved dinucleotide in the joiner linking domains 2 and 3 of a group II intron. RNA, 4, 151-166.
    • (1998) RNA , vol.4 , pp. 151-166
    • Podar, M.1    Zhou, J.2    Zhang, M.3    Franzen, J.S.4    Perlman, P.S.5    Peebles, C.L.6
  • 35
    • 0002319075 scopus 로고    scopus 로고
    • Catalytic reaction mechanisms and structural features of Group II intron ribozymes
    • Eckstein, F. and Lilley, D.M.J. (eds). Springer Verlag, New York
    • Pyle, A.M. (1996) Catalytic reaction mechanisms and structural features of Group II intron ribozymes. In Eckstein, F. and Lilley, D.M.J. (eds), Nucleic Acids and Molecular Biology. Vol. 10. Springer Verlag, New York, pp. 75-107.
    • (1996) Nucleic Acids and Molecular Biology , vol.10 , pp. 75-107
    • Pyle, A.M.1
  • 36
    • 0028351893 scopus 로고
    • Building a kinetic framework for group II intron ribozyme activity: Quantitation of interdomain binding and reaction rate
    • Pyle, A.M. and Green, J.B. (1994) Building a kinetic framework for group II intron ribozyme activity: quantitation of interdomain binding and reaction rate. Biochemistry, 33, 2716-2725.
    • (1994) Biochemistry , vol.33 , pp. 2716-2725
    • Pyle, A.M.1    Green, J.B.2
  • 37
    • 0026729278 scopus 로고
    • Ribozyme substrate binding site in the catalytic core of the Tetrahymena ribozyme
    • Pyle, A.M., Murphy, F.L. and Cech, T.R. (1992) Ribozyme substrate binding site in the catalytic core of the Tetrahymena ribozyme. Nature, 358, 123-128.
    • (1992) Nature , vol.358 , pp. 123-128
    • Pyle, A.M.1    Murphy, F.L.2    Cech, T.R.3
  • 38
    • 0030936233 scopus 로고    scopus 로고
    • Stopped-flow fluorescence spectrocopy reveals that domain 1 of a group II intron is an independent folding unit
    • Qin, P.Z.F. and Pyle, A.M. (1997) Stopped-flow fluorescence spectrocopy reveals that domain 1 of a group II intron is an independent folding unit Biochemistry, 36, 4718-4730.
    • (1997) Biochemistry , vol.36 , pp. 4718-4730
    • Qin, P.Z.F.1    Pyle, A.M.2
  • 39
    • 0032103821 scopus 로고    scopus 로고
    • The architectural organization and mechanistic function of group II intron structural elements
    • Qin, P.Z. and Pyle, A.M. (1998) The architectural organization and mechanistic function of group II intron structural elements. Curr. Opin. Struct. Biol., 8, 301-308.
    • (1998) Curr. Opin. Struct. Biol. , vol.8 , pp. 301-308
    • Qin, P.Z.1    Pyle, A.M.2
  • 40
    • 0030898510 scopus 로고    scopus 로고
    • A general purpose RNA-cleaving DNA enzyme
    • Santoro, S.W. and Joyce, G.F. (1997) A general purpose RNA-cleaving DNA enzyme. Proc. Natl Acad. Sci. USA, 94, 4262-4266.
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 4262-4266
    • Santoro, S.W.1    Joyce, G.F.2
  • 41
    • 0030965811 scopus 로고    scopus 로고
    • Defining the chemical groups essential for Tetrahymena aroup I intron function by nucleotide analog interference mapping (NAIM)
    • Strobel, S.A. and Shetty, K. (1997) Defining the chemical groups essential for Tetrahymena aroup I intron function by nucleotide analog interference mapping (NAIM). Proc. Natl Acad. Sci. USA, 94, 2903-2908.
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 2903-2908
    • Strobel, S.A.1    Shetty, K.2
  • 42
    • 0031984645 scopus 로고    scopus 로고
    • Complementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site
    • Strobel, S.A., Ortoleva-Donnelly, L., Ryder, S.P., Cate, J.H. and Moncoeur, E. (1998) Complementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site. Nature Struct. Biol., 5, 60-65.
    • (1998) Nature Struct. Biol. , vol.5 , pp. 60-65
    • Strobel, S.A.1    Ortoleva-Donnelly, L.2    Ryder, S.P.3    Cate, J.H.4    Moncoeur, E.5
  • 43
    • 0026409808 scopus 로고
    • Restoration of the sell-splicing activity of a defective group II intron by a small trans-acting RNA
    • Suchy, M. and Schmelzer, C. (1991) Restoration of the sell-splicing activity of a defective group II intron by a small trans-acting RNA. J. Mol. Biol., 222, 179-187.
    • (1991) J. Mol. Biol. , vol.222 , pp. 179-187
    • Suchy, M.1    Schmelzer, C.2
  • 44
    • 0032539968 scopus 로고    scopus 로고
    • The sequence-specificity of a group II intron ribozyme: Multiple mechanisms for promoting unusually high discrimination against mismatched targets
    • Xiang, Q., Qin, P.Z., Michels, W.J., Freeland, K. and Pyle, A.M. (1998) The sequence-specificity of a group II intron ribozyme: Multiple mechanisms for promoting unusually high discrimination against mismatched targets. Biochemistry, 37, 3839-3849.
    • (1998) Biochemistry , vol.37 , pp. 3839-3849
    • Xiang, Q.1    Qin, P.Z.2    Michels, W.J.3    Freeland, K.4    Pyle, A.M.5
  • 45
    • 0029312520 scopus 로고
    • Transfer RNA aminoacylation: Identification of a critical ribose 2′-hydroxyl-base interaction
    • Yap, L.-P. and Musier-Forsyth, K. (1995) Transfer RNA aminoacylation: Identification of a critical ribose 2′-hydroxyl-base interaction. RNA, 1, 418-124.
    • (1995) RNA , vol.1 , pp. 418-1124
    • Yap, L.-P.1    Musier-Forsyth, K.2


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