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Volumn 45, Issue 25, 2006, Pages 7861-7871

Evidence for preorganization of the glmS ribozyme ligand binding pocket

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; CROSSLINKING; ENZYMES; REACTION KINETICS; RNA;

EID: 33746920364     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi060337z     Document Type: Article
Times cited : (84)

References (55)
  • 1
    • 27144527479 scopus 로고    scopus 로고
    • Regulation of bacterial gene expression by riboswitches
    • Winkler, W. C., and Breaker, R. R. (2005) Regulation of bacterial gene expression by riboswitches, Annu. Rev. Microbiol. 59, 487-517.
    • (2005) Annu. Rev. Microbiol. , vol.59 , pp. 487-517
    • Winkler, W.C.1    Breaker, R.R.2
  • 3
    • 0346687595 scopus 로고    scopus 로고
    • The riboswitch control of bacterial metabolism
    • Nudler, E., and Mironov, A. S. (2004) The riboswitch control of bacterial metabolism, Trends Biochem. Sci. 29, 11-17.
    • (2004) Trends Biochem. Sci. , vol.29 , pp. 11-17
    • Nudler, E.1    Mironov, A.S.2
  • 4
    • 0038136962 scopus 로고    scopus 로고
    • Metabolite-binding RNA domains are present in the genes of eukaryotes
    • Sudarsan, N., Barrick, J. E., and Breaker, R. R. (2003) Metabolite-binding RNA domains are present in the genes of eukaryotes, RNA 9, 644-647.
    • (2003) RNA , vol.9 , pp. 644-647
    • Sudarsan, N.1    Barrick, J.E.2    Breaker, R.R.3
  • 5
    • 0037206833 scopus 로고    scopus 로고
    • Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression
    • Winkler, W., Nahvi, A., and Breaker, R. R. (2002) Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression, Nature 419, 952-956.
    • (2002) Nature , vol.419 , pp. 952-956
    • Winkler, W.1    Nahvi, A.2    Breaker, R.R.3
  • 7
    • 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. (2004) Control of gene expression by a natural metabolite-responsive ribozyme, Nature 428, 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
  • 8
    • 0037062949 scopus 로고    scopus 로고
    • The chemical repertoire of natural ribozymes
    • Doudna, J. A., and Cech, T. R. (2002) The chemical repertoire of natural ribozymes, Nature 418, 222-228.
    • (2002) Nature , vol.418 , pp. 222-228
    • Doudna, J.A.1    Cech, T.R.2
  • 9
    • 0025367254 scopus 로고
    • Self-splicing of group I introns
    • Cech, T. R. (1990) Self-splicing of group I introns, Annu. Rev. Biochem. 59, 543-568.
    • (1990) Annu. Rev. Biochem. , vol.59 , pp. 543-568
    • Cech, T.R.1
  • 10
    • 0025963132 scopus 로고
    • Visualizing the higher order folding of a catalytic RNA molecule
    • Celander, D. W., and Cech, T. R. (1991) Visualizing the higher order folding of a catalytic RNA molecule, Science 251, 401-407.
    • (1991) Science , vol.251 , pp. 401-407
    • Celander, D.W.1    Cech, T.R.2
  • 12
    • 33644852509 scopus 로고    scopus 로고
    • Core requirements for glmS ribozyme self-cleavage reveal a putative pseudoknot structure
    • Soukup, G. A. (2006) Core requirements for glmS ribozyme self-cleavage reveal a putative pseudoknot structure, Nucleic Acids Res. 34, 968-975.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 968-975
    • Soukup, G.A.1
  • 13
    • 28344457265 scopus 로고    scopus 로고
    • A pseudoknot in the 3′ non-core region of the glmS ribozyme enhances self-cleavage activity
    • Wilkinson, S. R., and Been, M. D. (2005) A pseudoknot in the 3′ non-core region of the glmS ribozyme enhances self-cleavage activity, RNA 11, 1788-1794.
    • (2005) RNA , vol.11 , pp. 1788-1794
    • Wilkinson, S.R.1    Been, M.D.2
  • 14
    • 33645462033 scopus 로고    scopus 로고
    • Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions
    • Roth, A., Nahvi, A., Lee, M., Jona, I., and Breaker, R. R. (2006) Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions, RNA 12, 607-619.
    • (2006) RNA , vol.12 , pp. 607-619
    • Roth, A.1    Nahvi, A.2    Lee, M.3    Jona, I.4    Breaker, R.R.5
  • 17
    • 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. (2000) General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme, Science 287, 1493-1497.
    • (2000) Science , vol.287 , pp. 1493-1497
    • Nakano, S.1    Chadalavada, D.M.2    Bevilacqua, P.C.3
  • 19
    • 24644454458 scopus 로고    scopus 로고
    • General acid catalysis by the hepatitis delta virus ribozyme
    • Das, S. R., and Piccirilli, J. A. (2005) General acid catalysis by the hepatitis delta virus ribozyme, Nat. Chem. Biol. 1, 45-52.
    • (2005) Nat. Chem. Biol. , vol.1 , pp. 45-52
    • Das, S.R.1    Piccirilli, J.A.2
  • 20
    • 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. (1999) Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme, Science 286, 123-126.
    • (1999) Science , vol.286 , pp. 123-126
    • Perrotta, A.T.1    Shih, I.2    Been, M.D.3
  • 21
    • 0035852640 scopus 로고    scopus 로고
    • Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage
    • Shih, I. H., and Been, M. D. (2001) Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage, Proc. Natl. Acad. Sci. U.S.A. 98, 1489-1494.
    • (2001) Proc. Natl. Acad. Sci. U.S.A. , vol.98 , pp. 1489-1494
    • Shih, I.H.1    Been, M.D.2
  • 22
    • 0034607544 scopus 로고    scopus 로고
    • Probing non-selective cation binding in the hairpin ribozyme with Tb(III)
    • Walter, N. G., Yang, N., and Burke, J. M. (2000) Probing non-selective cation binding in the hairpin ribozyme with Tb(III), J. Mol. Biol. 298, 539-555.
    • (2000) J. Mol. Biol. , vol.298 , pp. 539-555
    • Walter, N.G.1    Yang, N.2    Burke, J.M.3
  • 23
    • 0024819449 scopus 로고
    • Synthesis of small RNAs using T7 RNA polymerase
    • Milligan, J. F., and Uhlenbeck, O. C. (1989) Synthesis of small RNAs using T7 RNA polymerase, Methods Enzymol. 180, 51-62.
    • (1989) Methods Enzymol. , vol.180 , pp. 51-62
    • Milligan, J.F.1    Uhlenbeck, O.C.2
  • 24
    • 0027248444 scopus 로고
    • Novel RNA polymerization reaction catalyzed by a group I ribozyme
    • Chowrira, B. M., Berzal-Herranz, A., and Burke, J. M. (1993) Novel RNA polymerization reaction catalyzed by a group I ribozyme, EMBO J. 12, 3599-3605.
    • (1993) EMBO J. , vol.12 , pp. 3599-3605
    • Chowrira, B.M.1    Berzal-Herranz, A.2    Burke, J.M.3
  • 25
    • 0018877893 scopus 로고
    • Specific labeling of 3′ termini of RNA with T4 RNA ligase
    • England, T. E., Bruce, A. G., and Uhlenbeck, O. C. (1980) Specific labeling of 3′ termini of RNA with T4 RNA ligase, Methods Enzymol. 65, 65-74.
    • (1980) Methods Enzymol. , vol.65 , pp. 65-74
    • England, T.E.1    Bruce, A.G.2    Uhlenbeck, O.C.3
  • 26
    • 0034812874 scopus 로고    scopus 로고
    • Catalytic and structural assays for the hairpin ribozyme
    • Hampel, K. J., Pinard, R., and Burke, J. M. (2001) Catalytic and structural assays for the hairpin ribozyme, Methods Enzymol. 341, 566-580.
    • (2001) Methods Enzymol. , vol.341 , pp. 566-580
    • Hampel, K.J.1    Pinard, R.2    Burke, J.M.3
  • 27
    • 0037461285 scopus 로고    scopus 로고
    • Solvent protection of the hammerhead ribozyme in the ground state: Evidence for a cation-assisted conformational change leading to catalysis
    • Hampel, K. J., and Burke, J. M. (2003) Solvent protection of the hammerhead ribozyme in the ground state: Evidence for a cation-assisted conformational change leading to catalysis, Biochemistry 42, 4421-4429.
    • (2003) Biochemistry , vol.42 , pp. 4421-4429
    • Hampel, K.J.1    Burke, J.M.2
  • 28
    • 0033605919 scopus 로고    scopus 로고
    • Alignment of the two domains of the hairpin ribozyme-substrate complex defined by interdomain photoaffinity crosslinking
    • Pinard, R., Heckman, J. E., and Burke, J. M. (1999) Alignment of the two domains of the hairpin ribozyme-substrate complex defined by interdomain photoaffinity crosslinking, J. Mol. Biol. 287, 239-251.
    • (1999) J. Mol. Biol. , vol.287 , pp. 239-251
    • Pinard, R.1    Heckman, J.E.2    Burke, J.M.3
  • 29
    • 0347993061 scopus 로고    scopus 로고
    • In vitro selection of second site revenants analysis of the hairpin ribozyme active site
    • Sargueil, B., Hampel, K. J., Lambert, D., and Burke, J. M. (2003) In vitro selection of second site revenants analysis of the hairpin ribozyme active site, J. Biol. Chem. 278, 52783-52791.
    • (2003) J. Biol. Chem. , vol.278 , pp. 52783-52791
    • Sargueil, B.1    Hampel, K.J.2    Lambert, D.3    Burke, J.M.4
  • 30
    • 0022382116 scopus 로고
    • Iron(II) EDTA used to measure the helical twist along any DNA molecule
    • Tullius, T. D., and Dombroski, B. A. (1985) Iron(II) EDTA used to measure the helical twist along any DNA molecule, Science 230, 679-681.
    • (1985) Science , vol.230 , pp. 679-681
    • Tullius, T.D.1    Dombroski, B.A.2
  • 31
    • 0023623752 scopus 로고
    • Hydroxyl radical footprinting: A high-resolution method for mapping protein-DNA contacts
    • Tullius, T. D., Dombroski, B. A., Churchill, M. E., and Kam, L. (1987) Hydroxyl radical footprinting: A high-resolution method for mapping protein-DNA contacts, Methods Enzymol. 155, 537-558.
    • (1987) Methods Enzymol. , vol.155 , pp. 537-558
    • Tullius, T.D.1    Dombroski, B.A.2    Churchill, M.E.3    Kam, L.4
  • 32
    • 0032544035 scopus 로고    scopus 로고
    • DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone
    • Balasubramanian, B., Pogozelski, W. K., and Tullius, T. D. (1998) DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone, Proc. Natl. Acad. Sci. U.S.A. 95, 9738-9743.
    • (1998) Proc. Natl. Acad. Sci. U.S.A. , vol.95 , pp. 9738-9743
    • Balasubramanian, B.1    Pogozelski, W.K.2    Tullius, T.D.3
  • 33
    • 0025023607 scopus 로고
    • Iron(II)-ethylenediaminetetraacetic acid-catalyzed cleavage of RNA and DNA oligonucleotides: Similar reactivity toward single- and double-stranded forms
    • Celander, D. W., and Cech, T. R. (1990) Iron(II)- ethylenediaminetetraacetic acid-catalyzed cleavage of RNA and DNA oligonucleotides: Similar reactivity toward single- and double-stranded forms, Biochemistry 29, 1355-1361.
    • (1990) Biochemistry , vol.29 , pp. 1355-1361
    • Celander, D.W.1    Cech, T.R.2
  • 34
    • 0027990605 scopus 로고
    • Use of photoaffinity crosslinking and molecular modeling to analyze the global architecture of ribonuclease P RNA
    • Harris, M. E., Nolan, J. M., Malhotra, A., Brown, J. W., Harvey, S. C., and Pace, N. R. (1994) Use of photoaffinity crosslinking and molecular modeling to analyze the global architecture of ribonuclease P RNA, EMBO J. 13, 3953-3963.
    • (1994) EMBO J. , vol.13 , pp. 3953-3963
    • Harris, M.E.1    Nolan, J.M.2    Malhotra, A.3    Brown, J.W.4    Harvey, S.C.5    Pace, N.R.6
  • 35
    • 0029947541 scopus 로고    scopus 로고
    • Folding of the HDV antigenomic ribozyme pseudoknot structure deduced from long-range photocrosslinks
    • Bravo, C., Lescure, F., Laugaa, P., Fourrey, J. L., and Favre, A. (1996) Folding of the HDV antigenomic ribozyme pseudoknot structure deduced from long-range photocrosslinks, Nucleic Acids Res. 24, 1351-1359.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 1351-1359
    • Bravo, C.1    Lescure, F.2    Laugaa, P.3    Fourrey, J.L.4    Favre, A.5
  • 36
    • 0035957257 scopus 로고    scopus 로고
    • A conformational change in the "loop E-like" motif of the hairpin ribozyme is coincidental with domain docking and is essential for catalysis
    • Hampel, K. J., and Burke, J. M. (2001) A conformational change in the "loop E-like" motif of the hairpin ribozyme is coincidental with domain docking and is essential for catalysis, Biochemistry 40, 3723-3729.
    • (2001) Biochemistry , vol.40 , pp. 3723-3729
    • Hampel, K.J.1    Burke, J.M.2
  • 37
    • 0037009368 scopus 로고    scopus 로고
    • 4-Thio-U cross-linking identifies the active site of the VS ribozyme
    • Hiley, S. L., Sood, V. D., Fan, J., and Collins, R. A. (2002) 4-Thio-U cross-linking identifies the active site of the VS ribozyme, EMBO J. 21, 4691-4698.
    • (2002) EMBO J. , vol.21 , pp. 4691-4698
    • Hiley, S.L.1    Sood, V.D.2    Fan, J.3    Collins, R.A.4
  • 38
    • 15544362876 scopus 로고    scopus 로고
    • Photo-crosslinking detects a compact, active structure of the hammerhead ribozyme
    • Heckman, J. E., Lambert, D., and Burke, J. M. (2005) Photo-crosslinking detects a compact, active structure of the hammerhead ribozyme, Biochemistry 44, 4148-4156.
    • (2005) Biochemistry , vol.44 , pp. 4148-4156
    • Heckman, J.E.1    Lambert, D.2    Burke, J.M.3
  • 39
    • 0025129447 scopus 로고
    • Mapping the active site of ribonuclease P RNA using a substrate containing a photoaffinity agent
    • Burgin, A. B., and Pace, N. R. (1990) Mapping the active site of ribonuclease P RNA using a substrate containing a photoaffinity agent, EMBO J. 9, 4111-4118.
    • (1990) EMBO J. , vol.9 , pp. 4111-4118
    • Burgin, A.B.1    Pace, N.R.2
  • 40
    • 0022423644 scopus 로고
    • Investigation of the tertiary folding of Escherichia coli 16S RNA by in situ intra-RNA cross-linking within 30S ribosomal subunits
    • Atmadja, J., Brimacombe, R., Blocker, H., and Frank, R. (1985) Investigation of the tertiary folding of Escherichia coli 16S RNA by in situ intra-RNA cross-linking within 30S ribosomal subunits, Nucleic Acids Res. 13, 6919-6936.
    • (1985) Nucleic Acids Res. , vol.13 , pp. 6919-6936
    • Atmadja, J.1    Brimacombe, R.2    Blocker, H.3    Frank, R.4
  • 41
    • 0030805544 scopus 로고    scopus 로고
    • Dynamics of thermal motions within a large catalytic RNA investigated by cross-linking with thiol-disulfide interchange
    • Cohen, S. B., and Cech, T. R. (1997) Dynamics of thermal motions within a large catalytic RNA investigated by cross-linking with thiol-disulfide interchange, J. Am. Chem. Soc. 119, 6259-6268.
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 6259-6268
    • Cohen, S.B.1    Cech, T.R.2
  • 42
    • 0032549780 scopus 로고    scopus 로고
    • RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting
    • Sclavi, B., Sullivan, M., Chance, M. R., Brenowitz, M., and Woodson, S. A. (1998) RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting, Science 279, 1940-1943.
    • (1998) Science , vol.279 , pp. 1940-1943
    • Sclavi, B.1    Sullivan, M.2    Chance, M.R.3    Brenowitz, M.4    Woodson, S.A.5
  • 43
    • 19644391548 scopus 로고    scopus 로고
    • Model for general acid-base catalysis by the hammerhead ribozyme: PH-activity relationships of G8 and G12 variants at the putative active site
    • Han, J., and Burke, J. M. (2005) Model for general acid-base catalysis by the hammerhead ribozyme: pH-activity relationships of G8 and G12 variants at the putative active site, Biochemistry 44, 7864-7870.
    • (2005) Biochemistry , vol.44 , pp. 7864-7870
    • Han, J.1    Burke, J.M.2
  • 44
    • 4644305780 scopus 로고    scopus 로고
    • Architecture of a Diels-Alderase ribozyme with a preformed catalytic pocket
    • Keiper, S., Bebenroth, D., Seelig, B., Westhof, E., and Jaschke, A. (2004) Architecture of a Diels-Alderase ribozyme with a preformed catalytic pocket, Chem. Biol. 11, 1217-1227.
    • (2004) Chem. Biol. , vol.11 , pp. 1217-1227
    • Keiper, S.1    Bebenroth, D.2    Seelig, B.3    Westhof, E.4    Jaschke, A.5
  • 46
    • 0032559232 scopus 로고    scopus 로고
    • Induced folding in RNA-protein recognition: More than a simple molecular handshake
    • Frankel, A. D., and Smith, C. A. (1998) Induced folding in RNA-protein recognition: More than a simple molecular handshake, Cell 92, 149-151.
    • (1998) Cell , vol.92 , pp. 149-151
    • Frankel, A.D.1    Smith, C.A.2
  • 47
    • 0033784534 scopus 로고    scopus 로고
    • Induced fit in RNA-protein recognition
    • Williamson, J. R. (2000) Induced fit in RNA-protein recognition, Nat. Struct. Biol. 7, 834-837.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 834-837
    • Williamson, J.R.1
  • 49
    • 9244225713 scopus 로고    scopus 로고
    • Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine
    • Batey, R. T., Gilbert, S. D., and Montange, R. K. (2004) Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine, Nature 432, 411-415.
    • (2004) Nature , vol.432 , pp. 411-415
    • Batey, R.T.1    Gilbert, S.D.2    Montange, R.K.3
  • 50
    • 0030221025 scopus 로고    scopus 로고
    • Aptamer structures from A to zeta
    • Feigon, J., Dieckmann, T., and Smith, F. W. (1996) Aptamer structures from A to zeta, Chem. Biol. 3, 611-617.
    • (1996) Chem. Biol. , vol.3 , pp. 611-617
    • Feigon, J.1    Dieckmann, T.2    Smith, F.W.3
  • 51
    • 0037330568 scopus 로고    scopus 로고
    • Encapsulating streptomycin within a small 40-mer RNA
    • Tereshko, V., Skripkin, E., and Patel, D. J. (2003) Encapsulating streptomycin within a small 40-mer RNA, Chem. Biol. 10, 175-187.
    • (2003) Chem. Biol. , vol.10 , pp. 175-187
    • Tereshko, V.1    Skripkin, E.2    Patel, D.J.3
  • 52
    • 0031152162 scopus 로고    scopus 로고
    • Structural analysis of nucleic acid aptamers
    • Patel, D. J. (1997) Structural analysis of nucleic acid aptamers, Curr. Opin. Chem. Biol. 1, 32-46.
    • (1997) Curr. Opin. Chem. Biol. , vol.1 , pp. 32-46
    • Patel, D.J.1
  • 53
    • 0035848837 scopus 로고    scopus 로고
    • Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis
    • Rupert, P. B., and Ferre-D'Amare, A. R. (2001) Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis, Nature 410, 780-786.
    • (2001) Nature , vol.410 , pp. 780-786
    • Rupert, P.B.1    Ferre-D'Amare, A.R.2
  • 54
    • 0028294458 scopus 로고
    • Involvement of a GNRA tetraloop in long-range RNA tertiary interactions
    • Jaeger, L., Michel, F., and Westhof, E. (1994) Involvement of a GNRA tetraloop in long-range RNA tertiary interactions, J. Mol. Biol. 236, 1271-1276.
    • (1994) J. Mol. Biol. , vol.236 , pp. 1271-1276
    • Jaeger, L.1    Michel, F.2    Westhof, E.3
  • 55
    • 0030959348 scopus 로고    scopus 로고
    • Rules for RNA recognition of GNRA tetraloops deduced by in vitro selection: Comparison with in vivo evolution
    • Costa, M., and Michel, F. (1997) Rules for RNA recognition of GNRA tetraloops deduced by in vitro selection: Comparison with in vivo evolution, EMBO J. 16, 3289-3302.
    • (1997) EMBO J. , vol.16 , pp. 3289-3302
    • Costa, M.1    Michel, F.2


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