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Volumn 13, Issue 12, 2007, Pages 2098-2107

The 1.3 Å resolution structure of the RNA tridecamer r(GCGUUUGAAACGC): Metal ion binding correlates with base unstacking and groove contraction

Author keywords

Asymmetry; Electrostatic; Monovalent cations; X ray crystallography

Indexed keywords

METAL ION; RNA; SODIUM ION; DIVALENT CATION; METAL; OLIGORIBONUCLEOTIDE;

EID: 36248966494     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.730207     Document Type: Article
Times cited : (15)

References (44)
  • 1
    • 0346366808 scopus 로고    scopus 로고
    • 2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations
    • 2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations. J. Mol. Biol. 335: 555-571.
    • (2004) J. Mol. Biol , vol.335 , pp. 555-571
    • Auffinger, P.1    Bielecki, L.2    Westhof, E.3
  • 2
    • 0043163762 scopus 로고    scopus 로고
    • Microenvironment analysis and identification of magnesium binding sites in RNA
    • doi: 10.1093/nar/gkg471
    • Banatao, D.R., Altman, R.B., and Klein, T.E. 2003. Microenvironment analysis and identification of magnesium binding sites in RNA. Nucleic Acids Res. 31: 4450-4460. doi: 10.1093/nar/gkg471.
    • (2003) Nucleic Acids Res , vol.31 , pp. 4450-4460
    • Banatao, D.R.1    Altman, R.B.2    Klein, T.E.3
  • 4
    • 0034681490 scopus 로고    scopus 로고
    • Crystal structure of the ribonucleoprotein core of the signal recognition particle
    • Batey, R.T., Rambo, R.P., Lucast, L., Rha, B., and Doudna, J.A. 2000. Crystal structure of the ribonucleoprotein core of the signal recognition particle. Science 287: 1232-1239.
    • (2000) Science , vol.287 , pp. 1232-1239
    • Batey, R.T.1    Rambo, R.P.2    Lucast, L.3    Rha, B.4    Doudna, J.A.5
  • 7
    • 34249898353 scopus 로고    scopus 로고
    • +-induced changes in the HIV-1 TAR conformational dynamics using NMR residual dipolar coupling; new insights into the role of the counterions and electrostatic interactions in adaptative recognition
    • +-induced changes in the HIV-1 TAR conformational dynamics using NMR residual dipolar coupling; new insights into the role of the counterions and electrostatic interactions in adaptative recognition. Biochemistry 46: 6525-6535.
    • (2007) Biochemistry , vol.46 , pp. 6525-6535
    • Casiano-Negroni, A.1    Sun, X.2    Al-Hashimi, H.M.3
  • 8
    • 0030587890 scopus 로고    scopus 로고
    • Metal-binding sites in the major groove of a large ribozyme domain
    • Cate, J.H. and Doudna, J. 1996. Metal-binding sites in the major groove of a large ribozyme domain. Structure 4: 1221-1229.
    • (1996) Structure , vol.4 , pp. 1221-1229
    • Cate, J.H.1    Doudna, J.2
  • 9
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • Collaborative Computing Project 4
    • Collaborative Computing Project 4. 1994. The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50: 760-763.
    • (1994) Acta Crystallogr. D Biol. Crystallogr , vol.50 , pp. 760-763
  • 10
    • 36248991032 scopus 로고    scopus 로고
    • Collin, R.L. and Willis, M. 1971. The crystal structure of disodium dihydrogen hypophosphate hexahydrate (Na2H2P 2O6·6H2O) and disodium dihydrogen pyrophosphate hexahydrate Na2H2 P2O 7·6H2O, Acta Crystallogr. B 27: 291-302
    • 2O). Acta Crystallogr. B 27: 291-302.
  • 12
    • 0030856333 scopus 로고    scopus 로고
    • Metals, motifs and recognition in the crystal structure of a 5S rRNA domain
    • Correl, C.C., Freeborn, B., Moore, P.B., and Steitz, T.A. 1997. Metals, motifs and recognition in the crystal structure of a 5S rRNA domain. Cell 91: 705-712.
    • (1997) Cell , vol.91 , pp. 705-712
    • Correl, C.C.1    Freeborn, B.2    Moore, P.B.3    Steitz, T.A.4
  • 16
    • 0036024507 scopus 로고    scopus 로고
    • X-ray induced debromination of nucleic acids at the Br K absorption edge and implication for MAD phasing
    • Ennifar, E., Carpentier, P., Ferrer, J.-L., Walter, P., and Dumas, P. 2002. X-ray induced debromination of nucleic acids at the Br K absorption edge and implication for MAD phasing. Acta Crystallogr. D Biol. Crystallogr. 58: 1262-1268.
    • (2002) Acta Crystallogr. D Biol. Crystallogr , vol.58 , pp. 1262-1268
    • Ennifar, E.1    Carpentier, P.2    Ferrer, J.-L.3    Walter, P.4    Dumas, P.5
  • 17
    • 0038719800 scopus 로고    scopus 로고
    • A crystallographic study of the binding of 13 metal ions to two related RNA duplexes
    • doi: 10.1093/nar/gkg350
    • Ennifar, E., Walter, P., and Dumas, P. 2003. A crystallographic study of the binding of 13 metal ions to two related RNA duplexes. Nucleic Acids Res. 10: 2671-2682. doi: 10.1093/nar/gkg350.
    • (2003) Nucleic Acids Res , vol.10 , pp. 2671-2682
    • Ennifar, E.1    Walter, P.2    Dumas, P.3
  • 18
    • 0032532765 scopus 로고    scopus 로고
    • Exploration of metal ion binding sites in RNA folds by Brownian-dynamics simulations
    • Hermann, T. and Westhof, E. 1998. Exploration of metal ion binding sites in RNA folds by Brownian-dynamics simulations. Structure 6: 1303-1314.
    • (1998) Structure , vol.6 , pp. 1303-1314
    • Hermann, T.1    Westhof, E.2
  • 19
    • 0034624979 scopus 로고    scopus 로고
    • The crystal structure of the Rev binding element of HIV-1 reveals novel base pairing and conformational variability
    • Hung, L.-W., Holbrook, E.L., and Holbrook, S.R. 2000. The crystal structure of the Rev binding element of HIV-1 reveals novel base pairing and conformational variability. Proc. Natl. Acad. Sci. 97: 5107-5112.
    • (2000) Proc. Natl. Acad. Sci , vol.97 , pp. 5107-5112
    • Hung, L.-W.1    Holbrook, E.L.2    Holbrook, S.R.3
  • 20
    • 0034723137 scopus 로고    scopus 로고
    • The structure of the HIV-1 RRE high affinity Rev binding site at 1.6 Å resolution
    • Ippolito, J.A. and Steitz, T. 2000. The structure of the HIV-1 RRE high affinity Rev binding site at 1.6 Å resolution. J. Mol. Biol. 295: 711-717.
    • (2000) J. Mol. Biol , vol.295 , pp. 711-717
    • Ippolito, J.A.1    Steitz, T.2
  • 21
    • 0017361887 scopus 로고
    • A crystallographic study of metal-binding to yeast phenylalanine transfer RNA
    • Jack, A., Ladner, J.E., Rhodes, D., Brown, R.S., and Klug, A. 1977. A crystallographic study of metal-binding to yeast phenylalanine transfer RNA. J. Mol. Biol. 111: 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
  • 22
    • 84889120137 scopus 로고
    • Improved methods for building models in electron density maps and the location of errors in these models
    • Jones, T.A., Zou, J.Y., Cowan, S.W., and Kjeldgaard, M. 1991. Improved methods for building models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47: 110-119.
    • (1991) Acta Crystallogr. A , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou, J.Y.2    Cowan, S.W.3    Kjeldgaard, M.4
  • 23
    • 0026666130 scopus 로고
    • A trinucleotide can promote metal-ion-dependent specific cleavage of RNA
    • Kazakov, S. and Altman, S. 1992. A trinucleotide can promote metal-ion-dependent specific cleavage of RNA. Proc. Natl. Acad. Sci. 89: 7939-7943.
    • (1992) Proc. Natl. Acad. Sci , vol.89 , pp. 7939-7943
    • Kazakov, S.1    Altman, S.2
  • 24
    • 34447260753 scopus 로고    scopus 로고
    • A general strategy to solve the phase problem in RNA crystallography
    • Keel, A., Rambo, R., Batey, R., and Kieft, J. 2007. A general strategy to solve the phase problem in RNA crystallography. Structure 15: 761-772.
    • (2007) Structure , vol.15 , pp. 761-772
    • Keel, A.1    Rambo, R.2    Batey, R.3    Kieft, J.4
  • 26
    • 4344569647 scopus 로고    scopus 로고
    • The contribution of metal ions to the structural stability of the large ribosomal subunit
    • Klein, D., Moore, P.B., and Steitz, T.A. 2004. The contribution of metal ions to the structural stability of the large ribosomal subunit. RNA 10: 1366-1379.
    • (2004) RNA , vol.10 , pp. 1366-1379
    • Klein, D.1    Moore, P.B.2    Steitz, T.A.3
  • 27
    • 0242720648 scopus 로고    scopus 로고
    • An unusual sugar conformation in the structure of an RNA/DNA decamer of the polypurine tract may affect recognition by RNase H
    • Kopka, M.L., Lavelle, L., Han, G.W., Ng, H.-L., and Dickerson, R.E. 2003. An unusual sugar conformation in the structure of an RNA/DNA decamer of the polypurine tract may affect recognition by RNase H. J. Mol. Biol. 334: 653-665.
    • (2003) J. Mol. Biol , vol.334 , pp. 653-665
    • Kopka, M.L.1    Lavelle, L.2    Han, G.W.3    Ng, H.-L.4    Dickerson, R.E.5
  • 28
    • 0034326860 scopus 로고    scopus 로고
    • 2+-GAAA ribozymes and the evolution of small ribozymes
    • doi: 10.1093/nar/28.21.4197
    • 2+-GAAA ribozymes and the evolution of small ribozymes. Nucleic Acids Res. 28: 4197-4206. doi: 10.1093/nar/28.21.4197.
    • (2000) Nucleic Acids Res , vol.28 , pp. 4197-4206
    • Kuo, T.C.1    Herrin, D.L.2
  • 29
    • 0242396923 scopus 로고    scopus 로고
    • 3DNA: A software for the analysis, the rebuilding and the vizualisation of three-dimensional nucleic acid structures
    • doi: 10.1093/nar/gkg680
    • Lu, X.-J. and Olson, W.K. 2003. 3DNA: A software for the analysis, the rebuilding and the vizualisation of three-dimensional nucleic acid structures. Nucleic Acids Res. 31: 5108-5121. doi: 10.1093/nar/gkg680.
    • (2003) Nucleic Acids Res , vol.31 , pp. 5108-5121
    • Lu, X.-J.1    Olson, W.K.2
  • 30
    • 33746228126 scopus 로고    scopus 로고
    • Tertiary contacts distant from the active site prime a ribozyme for catalysis
    • Martick, M. and Scott, W.G. 2006. Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell 126: 309-320.
    • (2006) Cell , vol.126 , pp. 309-320
    • Martick, M.1    Scott, W.G.2
  • 31
    • 0032079703 scopus 로고    scopus 로고
    • Hydration and recognition of methylated CpG steps in DNA
    • Mayer-Jung, C., Moras, D., and Timsit, Y. 1998. Hydration and recognition of methylated CpG steps in DNA. EMBO J. 17: 2709-2718.
    • (1998) EMBO J , vol.17 , pp. 2709-2718
    • Mayer-Jung, C.1    Moras, D.2    Timsit, Y.3
  • 33
    • 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
  • 34
    • 0038681084 scopus 로고    scopus 로고
    • Crystal structure of an RNA purine-rich tetraplex containing adenine tetrads: Implications for specific binding in RNA tetraplexes
    • Pan, B., Xiong, Y., Shi, K., Deng, J., and Sundaralingam, M. 2003. Crystal structure of an RNA purine-rich tetraplex containing adenine tetrads: Implications for specific binding in RNA tetraplexes. Structure 11: 815-823.
    • (2003) Structure , vol.11 , pp. 815-823
    • Pan, B.1    Xiong, Y.2    Shi, K.3    Deng, J.4    Sundaralingam, M.5
  • 35
    • 0036940303 scopus 로고    scopus 로고
    • Metal ions in the structure and function of RNA
    • Pyle, A.M. 2002. Metal ions in the structure and function of RNA. J. Biol. Inorg. Chem. 7: 679-690.
    • (2002) J. Biol. Inorg. Chem , vol.7 , pp. 679-690
    • Pyle, A.M.1
  • 36
    • 0014691399 scopus 로고
    • Stereochemistry of nucleic acids and their constituents. V. The crystal and molecular structure of a hydrated monosodium inosine 5′-phosphate. A commonly occurring unusual nucleotide in the anticodons of tRNA
    • Rao, S.T. and Sundaralingam, M. 1969. Stereochemistry of nucleic acids and their constituents. V. The crystal and molecular structure of a hydrated monosodium inosine 5′-phosphate. A commonly occurring unusual nucleotide in the anticodons of tRNA. J. Am. Chem. Soc. 91: 1210-1217.
    • (1969) J. Am. Chem. Soc , vol.91 , pp. 1210-1217
    • Rao, S.T.1    Sundaralingam, M.2
  • 37
    • 0017194965 scopus 로고
    • RNA double-helical fragments at atomic resolution: II. The crystal structure of sodium guanylyl-3′,5′-cytidine nonahydrate
    • Rosenberg, J.M., Seeman, N., Day, R.O., and Rich, A. 1976. RNA double-helical fragments at atomic resolution: II. The crystal structure of sodium guanylyl-3′,5′-cytidine nonahydrate. J. Mol. Biol. 104: 145-167.
    • (1976) J. Mol. Biol , vol.104 , pp. 145-167
    • Rosenberg, J.M.1    Seeman, N.2    Day, R.O.3    Rich, A.4
  • 39
    • 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
  • 41
    • 0002296754 scopus 로고    scopus 로고
    • Reverse transcriptase and the generation of retroviral DNA
    • eds. J.M. Coffin et al, pp, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
    • Telesnitsky, A. and Goff, S.P. 1997. Reverse transcriptase and the generation of retroviral DNA. In Retroviruses (eds. J.M. Coffin et al.), pp. 121-160. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
    • (1997) Retroviruses , pp. 121-160
    • Telesnitsky, A.1    Goff, S.P.2
  • 42
    • 0035283086 scopus 로고    scopus 로고
    • Detection of alkali metal ions in DNA crystals using the state-of-the-art X-ray diffraction experiments
    • doi: 10.1093/nar/29.5.1208
    • Tereshko, V., Wilds, C.J., Minasov, G., Prakash, T.P., Maier, M.A., Howard, A., Wawrzak, Z., Manoharan, M., and Egli, M. 2001. Detection of alkali metal ions in DNA crystals using the state-of-the-art X-ray diffraction experiments. Nucleic Acids Res. 29: 1208-1215. doi: 10.1093/nar/29.5.1208.
    • (2001) Nucleic Acids Res , vol.29 , pp. 1208-1215
    • Tereshko, V.1    Wilds, C.J.2    Minasov, G.3    Prakash, T.P.4    Maier, M.A.5    Howard, A.6    Wawrzak, Z.7    Manoharan, M.8    Egli, M.9
  • 43
    • 4043179941 scopus 로고    scopus 로고
    • DNA and its counterions: A molecular dynamics study
    • doi: 10.1093/nar/gkh765
    • Varnai, P. and Zakrzewska, C. 2004. DNA and its counterions: A molecular dynamics study. Nucleic Acids Res. 32: 4269-4280. doi: 10.1093/nar/gkh765.
    • (2004) Nucleic Acids Res , vol.32 , pp. 4269-4280
    • Varnai, P.1    Zakrzewska, C.2


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