메뉴 건너뛰기




Volumn 45, Issue 23, 2006, Pages 7140-7147

Three conserved guanosines approach the reaction site in native and minimal hammerhead ribozymes

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; CROSSLINKING; CRYSTAL STRUCTURE; PHOTOCHEMICAL REACTIONS; PHYSIOLOGY; RNA;

EID: 33745056478     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi052457x     Document Type: Article
Times cited : (27)

References (33)
  • 1
    • 0028063567 scopus 로고
    • Three-dimensional structure of a hammerhead ribozyme
    • Pley, H. W., Flaherty, K. M., and McKay, D. B. (1994) Three-dimensional structure of a hammerhead ribozyme, Nature 372, 68-74.
    • (1994) Nature , vol.372 , pp. 68-74
    • Pley, H.W.1    Flaherty, K.M.2    McKay, D.B.3
  • 2
    • 0029073091 scopus 로고
    • The crystal structure of an all-RNA hammerhead ribozyme: A proposed mechanism for RNA catalytic cleavage
    • Scott, W. G., Finch, J. T., and Klug, A. (1995) The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage, Cell 81, 991-1002.
    • (1995) Cell , vol.81 , pp. 991-1002
    • Scott, W.G.1    Finch, J.T.2    Klug, A.3
  • 3
    • 0042509891 scopus 로고    scopus 로고
    • A helical twist-induced conformational switch activates cleavage in the hammerhead ribozyme
    • Dunham, C. M., Murray, J. B., and Scott, W. G. (2003) A helical twist-induced conformational switch activates cleavage in the hammerhead ribozyme, J. Mol. Biol. 332, 327-336.
    • (2003) J. Mol. Biol. , vol.332 , pp. 327-336
    • Dunham, C.M.1    Murray, J.B.2    Scott, W.G.3
  • 4
    • 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
    • Murray, J. B., Dunham, C. M., and Scott, W. G. (2002) 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, 121-130.
    • (2002) J. Mol. Biol. , vol.315 , pp. 121-130
    • Murray, J.B.1    Dunham, C.M.2    Scott, W.G.3
  • 5
    • 0032831634 scopus 로고    scopus 로고
    • Relationship between internucleotide linkage geometry and the stability of RNA
    • Soukup, G. A., and Breaker, R. R. (1999) Relationship between internucleotide linkage geometry and the stability of RNA, RNA 5, 1308-1325.
    • (1999) RNA , vol.5 , pp. 1308-1325
    • Soukup, G.A.1    Breaker, R.R.2
  • 6
    • 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. (1998) The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone, Chem. Biol. 5, 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
  • 7
    • 0035001461 scopus 로고    scopus 로고
    • Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations
    • O'Rear, J. L., Wang, S., Feig, A. L., Beigelman, L., Uhlenbeck, O. C., and Herschlag, D. (2001) Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations, RNA 7, 537-545.
    • (2001) RNA , vol.7 , pp. 537-545
    • O'Rear, J.L.1    Wang, S.2    Feig, A.L.3    Beigelman, L.4    Uhlenbeck, O.C.5    Herschlag, D.6
  • 8
    • 0036606134 scopus 로고    scopus 로고
    • Existence of efficient divalent metal ion-catalyzed and inefficient divalent metal ion-independent channels in reactions catalyzed by a hammerhead ribozyme
    • Zhou, J. M., Zhou, D. M., Takagi, Y., Kasai, Y., Inoue, A., Baba, T., and Taira, K. (2002) Existence of efficient divalent metal ion-catalyzed and inefficient divalent metal ion-independent channels in reactions catalyzed by a hammerhead ribozyme, Nucleic Acids Res. 30, 2374-2382.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 2374-2382
    • Zhou, J.M.1    Zhou, D.M.2    Takagi, Y.3    Kasai, Y.4    Inoue, A.5    Baba, T.6    Taira, K.7
  • 9
    • 19644363114 scopus 로고    scopus 로고
    • The structure-function dilemma of the hammerhead ribozyme
    • Blount, K. F., and Uhlenbeck, O. C. (2005) The structure-function dilemma of the hammerhead ribozyme, Annu. Rev. Biophys. Biomol. Struct. 34, 415-440.
    • (2005) Annu. Rev. Biophys. Biomol. Struct. , vol.34 , pp. 415-440
    • Blount, K.F.1    Uhlenbeck, O.C.2
  • 10
    • 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
    • Wang, S., Karbstein, K., Peracchi, A., Beigelman, L., and Herschlag, D. (1999) Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate, Biochemistry 38, 14363-14378.
    • (1999) Biochemistry , vol.38 , pp. 14363-14378
    • Wang, S.1    Karbstein, K.2    Peracchi, A.3    Beigelman, L.4    Herschlag, D.5
  • 12
    • 0031860104 scopus 로고    scopus 로고
    • Cristallographic structures of the hammerhead ribozyme: Relationship to ribozyme folding and catalysis
    • Wedekind, J. E., and McKay, D. B. (1998) Cristallographic structures of the hammerhead ribozyme: relationship to ribozyme folding and catalysis, Annu. Rev. Biophys. Biomol. Struct. 27, 475-502.
    • (1998) Annu. Rev. Biophys. Biomol. Struct. , vol.27 , pp. 475-502
    • Wedekind, J.E.1    McKay, D.B.2
  • 14
    • 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
  • 15
    • 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
  • 16
    • 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
  • 18
    • 22244451704 scopus 로고    scopus 로고
    • A kissing-loop interaction in a hammerhead viroid RNA critical for its in vitro folding and in vivo viability
    • Gago, S., De la Pena, M., and Flores, R. (2005) A kissing-loop interaction in a hammerhead viroid RNA critical for its in vitro folding and in vivo viability, RNA, 1073-1083.
    • (2005) RNA , pp. 1073-1083
    • Gago, S.1    De La Pena, M.2    Flores, R.3
  • 19
    • 0043009734 scopus 로고    scopus 로고
    • Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity
    • Khvorova, A., Lescoute, A., Westhof, E., and Jayasena, S. D. (2003) Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity, Nat. Struct. Biol. 10, 708-712.
    • (2003) Nat. Struct. Biol. , vol.10 , pp. 708-712
    • Khvorova, A.1    Lescoute, A.2    Westhof, E.3    Jayasena, S.D.4
  • 20
    • 12844269766 scopus 로고    scopus 로고
    • Characterization of a native hammerhead ribozyme derived from schistosomes
    • Osborne, E. M., Schaak, J. E., and Derose, V. J. (2005) Characterization of a native hammerhead ribozyme derived from schistosomes, RNA 11, 187-196.
    • (2005) RNA , vol.11 , pp. 187-196
    • Osborne, E.M.1    Schaak, J.E.2    Derose, V.J.3
  • 22
    • 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. 257, 239-251.
    • (1999) J. Mol. Biol. , vol.257 , pp. 239-251
    • Pinard, R.1    Heckman, J.E.2    Burke, J.M.3
  • 23
    • 0033554861 scopus 로고    scopus 로고
    • Structure and recognition of sheared tandem G-A base pairs associated with human centromere DNA sequence at atomic resolution
    • Gao, Y. G., Robinson, H., Sanishvili, R., Joachimiak, A., and Wang, A. H. (1999) Structure and recognition of sheared tandem G-A base pairs associated with human centromere DNA sequence at atomic resolution, Biochemistry 38, 16452-16460.
    • (1999) Biochemistry , vol.38 , pp. 16452-16460
    • Gao, Y.G.1    Robinson, H.2    Sanishvili, R.3    Joachimiak, A.4    Wang, A.H.5
  • 24
    • 0035919726 scopus 로고    scopus 로고
    • AA.AG@helix.ends: A:A and A:G base-pairs at the ends of 16 S and 23 S rRNA helices
    • Elgavish, T., Cannone, J. J., Lee, J. C., Harvey, S. C., and Gutell, R. R. (2001) AA.AG@helix.ends: A:A and A:G base-pairs at the ends of 16 S and 23 S rRNA helices, J. Mol. Biol. 310, 735-753.
    • (2001) J. Mol. Biol. , vol.310 , pp. 735-753
    • Elgavish, T.1    Cannone, J.J.2    Lee, J.C.3    Harvey, S.C.4    Gutell, R.R.5
  • 25
    • 0030877619 scopus 로고    scopus 로고
    • Hammerhead ribozymes with a faster cleavage rate
    • Clouet-d'Orval, B., and Uhlenbeck, O. C. (1997) Hammerhead ribozymes with a faster cleavage rate, Biochemistry 36, 9087-9092.
    • (1997) Biochemistry , vol.36 , pp. 9087-9092
    • Clouet-D'Orval, B.1    Uhlenbeck, O.C.2
  • 26
  • 27
    • 0242500942 scopus 로고    scopus 로고
    • Restricting the conformational heterogeneity of RNA by specific incorporation of 8-bromoguanosine
    • Proctor, D. J., Kierzek, E., Kierzek, R., and Bevilacqua, P. C. (2003) Restricting the conformational heterogeneity of RNA by specific incorporation of 8-bromoguanosine, J. Am. Chem. Soc. 125, 2390-2391.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 2390-2391
    • Proctor, D.J.1    Kierzek, E.2    Kierzek, R.3    Bevilacqua, P.C.4
  • 28
    • 1242338125 scopus 로고    scopus 로고
    • Pyrrolo-dC and pyrrolo-C: Fluorescent analogs of cytidine and 2′-deoxycytidine for the study of oligonucleotides
    • Berry, D. A., Jung, K. Y., Wise, D. S., Sercel, A. D., Pearson, W. H., Mackie, H., Randolph, J. B., and Somers, R. L. (2004) Pyrrolo-dC and pyrrolo-C: fluorescent analogs of cytidine and 2′-deoxycytidine for the study of oligonucleotides, Tetrahedron Lett. 45, 2457-2461.
    • (2004) Tetrahedron Lett. , vol.45 , pp. 2457-2461
    • Berry, D.A.1    Jung, K.Y.2    Wise, D.S.3    Sercel, A.D.4    Pearson, W.H.5    Mackie, H.6    Randolph, J.B.7    Somers, R.L.8
  • 30
    • 0031882388 scopus 로고    scopus 로고
    • A two-metal ion mechanism operates in the hammerhead ribozyme-mediated cleavage of an RNA substrate
    • Lott, W. B., Pontius, B. W., and von Hippel, P. H. (1998) A two-metal ion mechanism operates in the hammerhead ribozyme-mediated cleavage of an RNA substrate, Proc. Natl. Acad. Sci. U.S.A. 95, 542-547.
    • (1998) Proc. Natl. Acad. Sci. U.S.A. , vol.95 , pp. 542-547
    • Lott, W.B.1    Pontius, B.W.2    Von Hippel, P.H.3
  • 31
    • 0032472205 scopus 로고    scopus 로고
    • Inhibition of the hammerhead ribozyme cleavage reaction by site-specific binding of Tb
    • Feig, A. L., Scott, W. G., and Uhlenbeck, O. C. (1998) Inhibition of the hammerhead ribozyme cleavage reaction by site- specific binding of Tb, Science 279, 81-84.
    • (1998) Science , vol.279 , pp. 81-84
    • Feig, A.L.1    Scott, W.G.2    Uhlenbeck, O.C.3
  • 32
    • 0033231004 scopus 로고    scopus 로고
    • Probing the binding of Tb(III) and Eu(III) to the hammerhead ribozyme using luminescence spectroscopy
    • Feig, A. L., Panek, M., Horrocks, W. D., Jr., and Uhlenbeck, O. C. (1999) Probing the binding of Tb(III) and Eu(III) to the hammerhead ribozyme using luminescence spectroscopy, Chem. Biol. 6, 801-810.
    • (1999) Chem. Biol. , vol.6 , pp. 801-810
    • Feig, A.L.1    Panek, M.2    Horrocks Jr., W.D.3    Uhlenbeck, O.C.4
  • 33
    • 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?
    • Murray, J. B., and Scott, W. G. (2000) Does a single metal ion bridge the A-9 and scissile phosphate groups in the catalytically active hammerhead ribozyme structure? J. Mol. Biol. 296, 33-41.
    • (2000) J. Mol. Biol. , vol.296 , pp. 33-41
    • Murray, J.B.1    Scott, W.G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.