메뉴 건너뛰기




Volumn 289, Issue 5, 1999, Pages 1267-1282

Solution structure and thermodynamics of a divalent metal ion binding site in an RNA pseudoknot

Author keywords

Frameshifting; Metal binding; NMR; Pseudoknot; RNA structure and thermodynamics

Indexed keywords

COBALT; DIVALENT CATION; HYDROXYL GROUP; MAGNESIUM ION; METAL ION; NITROGEN; OXYGEN; PHOSPHATE; PROTON;

EID: 0345299164     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2841     Document Type: Article
Times cited : (82)

References (61)
  • 1
    • 0028951325 scopus 로고
    • Divalent metal ion binding to a conserved wobble pair defining the upstream site of cleavage of group I self-splicing introns
    • Allain F. H. T., Varani G. Divalent metal ion binding to a conserved wobble pair defining the upstream site of cleavage of group I self-splicing introns. Nucl. Acids Res. 23:1995;341-350.
    • (1995) Nucl. Acids Res. , vol.23 , pp. 341-350
    • Allain, F.H.T.1    Varani, G.2
  • 3
    • 0344708691 scopus 로고
    • Interchange of hydrogen isotopes with complex salts. Part I. Kinetics of the interchange with the luteocobaltic complex
    • Anderson J. S., Briscoe H. V. A., Spoor N. L. Interchange of hydrogen isotopes with complex salts. Part I. Kinetics of the interchange with the luteocobaltic complex. J. Chem. Soc. 1943;361-367.
    • (1943) J. Chem. Soc. , pp. 361-367
    • Anderson, J.S.1    Briscoe, H.V.A.2    Spoor, N.L.3
  • 4
    • 0029091681 scopus 로고
    • Ribosomal frameshifting on viral RNAs
    • Brierley I. Ribosomal frameshifting on viral RNAs. J. Gen. Virol. 76:1995;1185-1892.
    • (1995) J. Gen. Virol. , vol.76 , pp. 1185-1892
    • Brierley, I.1
  • 5
    • 0025769767 scopus 로고
    • Mutational analysis of the RNA pseudoknot component of a coronavirus ribosomal frameshifting signal
    • Brierly I., Rolley N. J., Jenner A. J., Inglis S. C. Mutational analysis of the RNA pseudoknot component of a coronavirus ribosomal frameshifting signal. J. Mol. Biol. 220:1991;889-902.
    • (1991) J. Mol. Biol. , vol.220 , pp. 889-902
    • Brierly, I.1    Rolley, N.J.2    Jenner, A.J.3    Inglis, S.C.4
  • 7
    • 0030587890 scopus 로고    scopus 로고
    • Metal-binding sites in the major groove of a large ribozyme domain
    • Cate J. H., Doudna J. A. Metal-binding sites in the major groove of a large ribozyme domain. Structure. 4:1996;1221-1229.
    • (1996) Structure , vol.4 , pp. 1221-1229
    • Cate, J.H.1    Doudna, J.A.2
  • 9
    • 0026598965 scopus 로고
    • An RNA pseudoknot and an optimal heptameric shift site are required for highly efficient ribosomal frameshifting on a retroviral messenger RNA
    • Chamorro M., Parkin N., Varmus H. E. An RNA pseudoknot and an optimal heptameric shift site are required for highly efficient ribosomal frameshifting on a retroviral messenger RNA. Proc. Natl Acad. Sci. USA. 89:1992;713-717.
    • (1992) Proc. Natl Acad. Sci. USA , vol.89 , pp. 713-717
    • Chamorro, M.1    Parkin, N.2    Varmus, H.E.3
  • 10
    • 0028962374 scopus 로고
    • Structural and functional studies of retroviral RNA pseudoknots involved in ribosomal frameshifting: Nucleotides at the junction of the two stems are important for efficient ribosomal frameshifting
    • Chen X., Chamorro M., Lee S. I., Shen L. X., Hines J. V., Tinoco I. Jr, Varmus H. E. Structural and functional studies of retroviral RNA pseudoknots involved in ribosomal frameshifting: nucleotides at the junction of the two stems are important for efficient ribosomal frameshifting. EMBO J. 14:1995;842-852.
    • (1995) EMBO J. , vol.14 , pp. 842-852
    • Chen, X.1    Chamorro, M.2    Lee, S.I.3    Shen, L.X.4    Hines, J.V.5    Tinoco I., Jr.6    Varmus, H.E.7
  • 11
    • 0033516616 scopus 로고    scopus 로고
    • Structure and thermodynamics of metal binding in the P5 helix of a group I intron ribozyme
    • Colmenarejo G., Tinoco I. Jr. Structure and thermodynamics of metal binding in the P5 helix of a group I intron ribozyme. J. Mol. Biol. 1999.
    • (1999) J. Mol. Biol.
    • Colmenarejo, G.1    Tinoco I., Jr.2
  • 12
    • 0030856333 scopus 로고    scopus 로고
    • Metals, motifs, and recognition in the crystal structure of a 5 S rRNA domain
    • Correl C. C., Freeborn B., Moore P. B., Steitz T. A. Metals, motifs, and recognition in the crystal structure of a 5 S rRNA domain. Cell. 91:1997;705-712.
    • (1997) Cell , vol.91 , pp. 705-712
    • Correl, C.C.1    Freeborn, B.2    Moore, P.B.3    Steitz, T.A.4
  • 13
  • 15
    • 0026643735 scopus 로고
    • Ribosomal frameshifting efficiency and gag/gag-pol ratio are critical for yeast M1 double-stranded RNA virus propagation
    • Dinman J. D., Wickner R. B. Ribosomal frameshifting efficiency and gag/gag-pol ratio are critical for yeast M1 double-stranded RNA virus propagation. J. of Virol. 66:1992;3669-3676.
    • (1992) J. of Virol. , vol.66 , pp. 3669-3676
    • Dinman, J.D.1    Wickner, R.B.2
  • 18
    • 0031577308 scopus 로고    scopus 로고
    • Base-pairings within the RNA pseudoknot associated with the simian retrovirus-1 gag-pro frameshift site
    • Du Z. H., Holland J. A., Hansen M. R., Giedroc D. P., Hoffman D. W. Base-pairings within the RNA pseudoknot associated with the simian retrovirus-1 gag-pro frameshift site. J. Mol. Biol. 270:1997;464-470.
    • (1997) J. Mol. Biol. , vol.270 , pp. 464-470
    • Du, Z.H.1    Holland, J.A.2    Hansen, M.R.3    Giedroc, D.P.4    Hoffman, D.W.5
  • 19
    • 0002198148 scopus 로고    scopus 로고
    • The role of metal ions in RNA biochemistry
    • R. F. Gesteland, T. R. Cech, & J. F. Atkins. Plainview: Cold Spring Harbor Laboratory Press
    • Feig A. L., Uhlenbeck O. C. The role of metal ions in RNA biochemistry. Gesteland R. F., Cech T. R., Atkins J. F. The RNA World. 1999;287-318 Cold Spring Harbor Laboratory Press, Plainview.
    • (1999) The RNA World , pp. 287-318
    • Feig, A.L.1    Uhlenbeck, O.C.2
  • 20
    • 0032497521 scopus 로고    scopus 로고
    • Crystal structure of a hepatitis delta virus ribozyme
    • Ferré-D'Amaré A. R., Zhou K. H., Doudna J. A. 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.H.2    Doudna, J.A.3
  • 21
    • 0024294369 scopus 로고
    • Novel reactions of RNase P with a t-RNA like structure in turnip yellow mosaic virus RNA
    • Guerrier-Takada C., van Belkum A., Pleij C. W. A., Altman S. Novel reactions of RNase P with a t-RNA like structure in turnip yellow mosaic virus RNA. Cell. 53:1988;267-272.
    • (1988) Cell , vol.53 , pp. 267-272
    • Guerrier-Takada, C.1    Van Belkum, A.2    Pleij, C.W.A.3    Altman, S.4
  • 23
    • 0032532765 scopus 로고    scopus 로고
    • Exploration of metal ion binding sites in RNA folds by Brownian dynamics simulations
    • Hermann T., Westhof E. Exploration of metal ion binding sites in RNA folds by Brownian dynamics simulations. Structure. 6:1998;1303-1314.
    • (1998) Structure , vol.6 , pp. 1303-1314
    • Hermann, T.1    Westhof, E.2
  • 25
    • 0017361887 scopus 로고
    • A crystallographic study of metal-binding to yeast phenylalanine transfer RNA
    • Jack A., Ladner J. E., Rhodes D., Brown R. S., Klug A. A crystallographic study of metal-binding to yeast phenylalanine transfer RNA. J. Mol. Biol. 111:1977;315-328.
    • (1977) J. Mol. Biol. , vol.111 , pp. 315-328
    • Jack, A.1    Ladner, J.E.2    Rhodes, D.3    Brown, R.S.4    Klug, A.5
  • 26
    • 0024286617 scopus 로고
    • The secondary structure of ribonuclease P RNA, the catalytic element of a ribonucleoprotien enzyme
    • James B. D., Olsen G. J., Liu J., Pace N. R. The secondary structure of ribonuclease P RNA, the catalytic element of a ribonucleoprotien enzyme. Cell. 52:1988;19-26.
    • (1988) Cell , vol.52 , pp. 19-26
    • James, B.D.1    Olsen, G.J.2    Liu, J.3    Pace, N.R.4
  • 27
    • 0020655279 scopus 로고
    • T-RNA like structures of plant viral RNAs: Comformational requirements for adenylation and aminoacylation
    • Joshi R. L., Joshi S., Chapeville F., Haenni A. L. t-RNA like structures of plant viral RNAs: comformational requirements for adenylation and aminoacylation. EMBO J. 2:1983;1123-1127.
    • (1983) EMBO J. , vol.2 , pp. 1123-1127
    • Joshi, R.L.1    Joshi, S.2    Chapeville, F.3    Haenni, A.L.4
  • 28
    • 0000604820 scopus 로고
    • Ribonuclease-H activation by inert transition-metal complexes. Mechanistic probes for metallocofactors: Insights on the metallobiochemistry of divalent magnesium ion
    • Jou R. W., Cowan J. A. Ribonuclease-H activation by inert transition-metal complexes. Mechanistic probes for metallocofactors: insights on the metallobiochemistry of divalent magnesium ion. J. Am. Chem. Soc. 113:1991;6685-6686.
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 6685-6686
    • Jou, R.W.1    Cowan, J.A.2
  • 29
    • 0032563199 scopus 로고    scopus 로고
    • NMR structure determination of the binding site for ribosomal protein S8 from Escherichia coli 16 S rRNA
    • Kalurachchi K., Nikonowicz E. P. NMR structure determination of the binding site for ribosomal protein S8 from Escherichia coli 16 S rRNA. J. Mol. Biol. 280:1998;639-654.
    • (1998) J. Mol. Biol. , vol.280 , pp. 639-654
    • Kalurachchi, K.1    Nikonowicz, E.P.2
  • 30
    • 0030740427 scopus 로고    scopus 로고
    • A mutant pseudoknot that promotes ribosomal frameshifting in mouse mammary tumor virus
    • Kang H., Tinoco I. Jr. A mutant pseudoknot that promotes ribosomal frameshifting in mouse mammary tumor virus. Nucl. Acids Res. 25:1997;1943-1949.
    • (1997) Nucl. Acids Res. , vol.25 , pp. 1943-1949
    • Kang, H.1    Tinoco I., Jr.2
  • 31
    • 0030011355 scopus 로고    scopus 로고
    • Conformation of a non-frameshifting RNA pseudoknot from mouse mammary tumor virus
    • Kang H., Hines J. V., Tinoco I. Jr. Conformation of a non-frameshifting RNA pseudoknot from mouse mammary tumor virus. J. Mol. Biol. 259:1996;135-147.
    • (1996) J. Mol. Biol. , vol.259 , pp. 135-147
    • Kang, H.1    Hines, J.V.2    Tinoco I., Jr.3
  • 33
    • 0031570344 scopus 로고    scopus 로고
    • Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt(III)hexammine
    • Kieft J. S., Tinoco I. Jr. Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt(III)hexammine. Structure. 5:1997;713-721.
    • (1997) Structure , vol.5 , pp. 713-721
    • Kieft, J.S.1    Tinoco I., Jr.2
  • 34
    • 0032540504 scopus 로고    scopus 로고
    • NMR structure of a classical pseudoknot: Interplay of single- And double-stranded RNA
    • Kolk M. H., van der Graaf M., Wijimenga S. S., Pleij C. W., Heus H. A., Hilbers C. W. NMR structure of a classical pseudoknot: interplay of single- and double-stranded RNA. Science. 280:1998;434-438.
    • (1998) Science , vol.280 , pp. 434-438
    • Kolk, M.H.1    Van Der Graaf, M.2    Wijimenga, S.S.3    Pleij, C.W.4    Heus, H.A.5    Hilbers, C.W.6
  • 36
    • 0028239266 scopus 로고
    • Two major tertiary folding transitions of the Tetrahymena catalytic RNA
    • Laggerbauer B., Murphy F. L., Cech T. R. Two major tertiary folding transitions of the Tetrahymena catalytic RNA. EMBO J. 13:1984;2669-2676.
    • (1984) EMBO J. , vol.13 , pp. 2669-2676
    • Laggerbauer, B.1    Murphy, F.L.2    Cech, T.R.3
  • 38
    • 0023651444 scopus 로고
    • Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates
    • Milligan J. F., Groebe D. R., Witherell G. W., Uhlenbeck O. C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucl. Acids Res. 15:1987;8783-8798.
    • (1987) Nucl. Acids Res. , vol.15 , pp. 8783-8798
    • Milligan, J.F.1    Groebe, D.R.2    Witherell, G.W.3    Uhlenbeck, O.C.4
  • 39
    • 0023238983 scopus 로고
    • Interaction of antibiotics with functional sites in 16 S ribosomal RNA
    • Moazed D., Noller H. F. Interaction of antibiotics with functional sites in 16 S ribosomal RNA. Nature. 327:1987;389-394.
    • (1987) Nature , vol.327 , pp. 389-394
    • Moazed, D.1    Noller, H.F.2
  • 40
    • 0032542051 scopus 로고    scopus 로고
    • Equilibrium unfolding (folding) pathway of a model H-type pseudoknotted RNA: The role of magnesium ions in stability
    • Nixon P. L., Giedroc D. P. Equilibrium unfolding (folding) pathway of a model H-type pseudoknotted RNA: the role of magnesium ions in stability. Biochemistry. 37:1998;16116-16129.
    • (1998) Biochemistry , vol.37 , pp. 16116-16129
    • Nixon, P.L.1    Giedroc, D.P.2
  • 41
    • 0003156250 scopus 로고
    • Divalent metal ions in RNA folding and catalysis
    • R. F. Gesteland, & J. F. Atkins. Plainview: Cold Spring Harbor Laboratory Press
    • Pan T., Long D. M., Uhlenbeck O. C. Divalent metal ions in RNA folding and catalysis. Gesteland R. F., Atkins J. F. The RNA World. 1993;271-302 Cold Spring Harbor Laboratory Press, Plainview.
    • (1993) The RNA World , pp. 271-302
    • Pan, T.1    Long, D.M.2    Uhlenbeck, O.C.3
  • 42
    • 33845555707 scopus 로고
    • Exchangeable proton NMR without base-line distortion, using new strong-pulse sequences
    • Plateau P., Guéron M. Exchangeable proton NMR without base-line distortion, using new strong-pulse sequences. J. Am. Chem. Soc. 104:1982;7310-7311.
    • (1982) J. Am. Chem. Soc. , vol.104 , pp. 7310-7311
    • Plateau, P.1    Guéron, M.2
  • 43
    • 0022423219 scopus 로고
    • A new principle of RNA folding based on pseudoknotting
    • Pleij C. W. A., Rietveld K., Bosch L. A new principle of RNA folding based on pseudoknotting. Nucl. Acids Res. 13:1985;1717-1731.
    • (1985) Nucl. Acids Res. , vol.13 , pp. 1717-1731
    • Pleij, C.W.A.1    Rietveld, K.2    Bosch, L.3
  • 44
    • 0028063567 scopus 로고
    • Three-dimensional structure of a hammerhead ribozyme
    • Pley H. W., Flaherty K. M., McKay D. B. Three-dimensional structure of a hammerhead ribozyme. Nature. 372:1994;68-74.
    • (1994) Nature , vol.372 , pp. 68-74
    • Pley, H.W.1    Flaherty, K.M.2    McKay, D.B.3
  • 45
    • 0029975140 scopus 로고    scopus 로고
    • Thermodynamics of folding fo the RNA pseudoknot of the T4 gene 32 autoregulatory messenger RNA
    • Qui H., Kahuarachchi K., Du Z., Hoffman D. W., Giedroc D. P. Thermodynamics of folding fo the RNA pseudoknot of the T4 gene 32 autoregulatory messenger RNA. Biochemistry. 35:1996;4176-4186.
    • (1996) Biochemistry , vol.35 , pp. 4176-4186
    • Qui, H.1    Kahuarachchi, K.2    Du, Z.3    Hoffman, D.W.4    Giedroc, D.P.5
  • 46
    • 0020490476 scopus 로고
    • The t-RNA like structure at the 3′ terminus of turnip yellow mosaic virus RNA. Differences and similarities with canonical tRNA
    • Rietveld K., van Poelgeest R., Pleij C. W. A., van Boom J. H., Bosch L. The t-RNA like structure at the 3′ terminus of turnip yellow mosaic virus RNA. Differences and similarities with canonical tRNA. Nucl. Acids Res. 10:1982;1929-1946.
    • (1982) Nucl. Acids Res. , vol.10 , pp. 1929-1946
    • Rietveld, K.1    Van Poelgeest, R.2    Pleij, C.W.A.3    Van Boom, J.H.4    Bosch, L.5
  • 48
    • 0029932653 scopus 로고    scopus 로고
    • Neomycin, spermine, and hexamminecobalt (III) share common structural motiffs in converting B - To A -DNA
    • Robinson H., Wang A. H.-J. Neomycin, spermine, and hexamminecobalt (III) share common structural motiffs in converting B - to A -DNA. Nucl. Acids Res. 24:1996;676-682.
    • (1996) Nucl. Acids Res. , vol.24 , pp. 676-682
    • Robinson, H.1    Wang, A.H.-J.2
  • 50
    • 0028864098 scopus 로고
    • Synthesis and NMR of RNA with selective isotope enrichment in the bases
    • SantaLucia J., Shen L. X., Cai Z. P., Lewis H., Tinoco I. Jr. Synthesis and NMR of RNA with selective isotope enrichment in the bases. Nucl. Acids Res. 23:1995;4913-4921.
    • (1995) Nucl. Acids Res. , vol.23 , pp. 4913-4921
    • Santalucia, J.1    Shen, L.X.2    Cai, Z.P.3    Lewis, H.4    Tinoco I., Jr.5
  • 51
    • 0024411665 scopus 로고
    • RNA pseudoknots that interact with components of the translation apparatus
    • Schimmel P. RNA pseudoknots that interact with components of the translation apparatus. Cell. 58:1989;9-12.
    • (1989) Cell , vol.58 , pp. 9-12
    • Schimmel, P.1
  • 52
    • 0029073091 scopus 로고
    • Crystal structure of an all-RNA hammerhead ribozyme: A proposed mechanism for RNA catalytic cleavage
    • Scott W. G., Finch J. T., Klug A. Crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell. 81:1995;991-1002.
    • (1995) Cell , vol.81 , pp. 991-1002
    • Scott, W.G.1    Finch, J.T.2    Klug, A.3
  • 53
    • 0028910590 scopus 로고
    • The structure of an RNA pseudoknot that causes efficient frameshifting in mouse mammary tumor virus
    • Shen L. X., Tinoco I. Jr. The structure of an RNA pseudoknot that causes efficient frameshifting in mouse mammary tumor virus. J. Mol. Biol. 247:1995;963-978.
    • (1995) J. Mol. Biol. , vol.247 , pp. 963-978
    • Shen, L.X.1    Tinoco I., Jr.2
  • 54
    • 0017295709 scopus 로고
    • Conformational changes of transfer RNA. The role of magnesium (II)
    • Stein A., Crothers D. M. Conformational changes of transfer RNA. The role of magnesium (II). Biochemistry. 15:1976;160-167.
    • (1976) Biochemistry , vol.15 , pp. 160-167
    • Stein, A.1    Crothers, D.M.2
  • 55
    • 85030360038 scopus 로고    scopus 로고
    • A minor groove RNA triplex in the crystal structure of a viral pseudoknot involved in ribosomal frameshifting
    • Su L., Chen L., Egil M., Berger J. M., Rich A. A minor groove RNA triplex in the crystal structure of a viral pseudoknot involved in ribosomal frameshifting. Nature Struct. Biol. 1999.
    • (1999) Nature Struct. Biol.
    • Su, L.1    Chen, L.2    Egil, M.3    Berger, J.M.4    Rich, A.5
  • 56
    • 0024973814 scopus 로고
    • Unusual mRNA pseudoknot structure is recognized by a protein translational repressor
    • Tang C. K., Draper D. E. Unusual mRNA pseudoknot structure is recognized by a protein translational repressor. Cell. 57:1989;531-536.
    • (1989) Cell , vol.57 , pp. 531-536
    • Tang, C.K.1    Draper, D.E.2
  • 57
    • 0028307694 scopus 로고
    • Identification and analysis of the pseudoknot containing gag-pro ribosomal frameshift signal of simian retrovirus -1
    • ten Dam E., Brierly I., Inglis S., Pleij C. Identification and analysis of the pseudoknot containing gag-pro ribosomal frameshift signal of simian retrovirus -1. Nucl. Acids Res. 22:1994;2304-2310.
    • (1994) Nucl. Acids Res. , vol.22 , pp. 2304-2310
    • Ten Dam, E.1    Brierly, I.2    Inglis, S.3    Pleij, C.4
  • 58
    • 0029281776 scopus 로고
    • Analysis of the role of the pseudoknot component in the SRV-1 gag-pro ribosomal frameshift signal: Loop lengths and stability of the stem regions
    • ten Dam E. B., Verlaan P. W. G., Pleij C. W. A. Analysis of the role of the pseudoknot component in the SRV-1 gag-pro ribosomal frameshift signal: loop lengths and stability of the stem regions. RNA. 1:1995;146-154.
    • (1995) RNA , vol.1 , pp. 146-154
    • Ten Dam, E.B.1    Verlaan, P.W.G.2    Pleij, C.W.A.3
  • 59
    • 0032511143 scopus 로고    scopus 로고
    • Non-nearest neighbor effects on the thermodynamics of unfolding of a model mRNA pseudoknot
    • Theimer C. A., Wang Y., Hoffman D. W., Krisch H. M., Giedroc D. P. Non-nearest neighbor effects on the thermodynamics of unfolding of a model mRNA pseudoknot. J. Mol. Biol. 279:1998;545-564.
    • (1998) J. Mol. Biol. , vol.279 , pp. 545-564
    • Theimer, C.A.1    Wang, Y.2    Hoffman, D.W.3    Krisch, H.M.4    Giedroc, D.P.5
  • 60
    • 0025113514 scopus 로고
    • RNA pseudoknots-stability and loop size requirements
    • Wyatt J. R., Puglisi J. D., Tinoco I. Jr. RNA pseudoknots-stability and loop size requirements. J. Mol. Biol. 214:1990;455-470.
    • (1990) J. Mol. Biol. , vol.214 , pp. 455-470
    • Wyatt, J.R.1    Puglisi, J.D.2    Tinoco I., Jr.3
  • 61
    • 0025748046 scopus 로고
    • Synthesis and purification of large amounts of RNA oligonucleotides
    • Wyatt J. R., Chastain M., Puglisi J. D. Synthesis and purification of large amounts of RNA oligonucleotides. Biotechniques. 11:1991;764-769.
    • (1991) Biotechniques , vol.11 , pp. 764-769
    • Wyatt, J.R.1    Chastain, M.2    Puglisi, J.D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.