메뉴 건너뛰기




Volumn 280, Issue 4, 1998, Pages 639-654

NMR structure determination of the binding site for ribosomal protein S8 from Escherichia coli 16 S rRNA

Author keywords

Base triple; Conformational exchange; Magnesium ion; Protein RNA interaction; RNA structure

Indexed keywords

RIBOSOME PROTEIN; RNA 16S;

EID: 0032563199     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1915     Document Type: Article
Times cited : (24)

References (58)
  • 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. (1995a). 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, 341-350.
    • (1995) Nucl. Acids Res. , vol.23 , pp. 341-350
    • Allain, F.H.-T.1    Varani, G.2
  • 2
    • 0029082529 scopus 로고
    • Structure of the P1 helix from group I self-splicing introns. J
    • Allain, F. H.-T. & Varani, G. (1995b). Structure of the P1 helix from group I self-splicing introns. J. Mol. Biol. 250, 333-353.
    • (1995) Mol. Biol. , vol.250 , pp. 333-353
    • Allain, F.H.-T.1    Varani, G.2
  • 3
    • 0028111871 scopus 로고
    • Role of conserved nucleotides in building the 16 S rRNA binding site of E. coli ribosomal protein S8
    • Allmang, C., Mougel, M., Westhof, E., Ehresmann, B. & Ehresmann, C. (1994). Role of conserved nucleotides in building the 16 S rRNA binding site of E. coli ribosomal protein S8. Nucl. Acids Res. 22, 3708-3714.
    • (1994) Nucl. Acids Res. , vol.22 , pp. 3708-3714
    • Allmang, C.1    Mougel, M.2    Westhof, E.3    Ehresmann, B.4    Ehresmann, C.5
  • 4
    • 0027718102 scopus 로고
    • Nucleic acid structure analysis; a users guide to a collection of new analysis programs
    • Babcock, M. S., Pednault, E. P. & Olson, W. K. (1993). Nucleic acid structure analysis; a users guide to a collection of new analysis programs. J. Biomol. Struct. Dynam. 11, 597-628.
    • (1993) J. Biomol. Struct. Dynam. , vol.11 , pp. 597-628
    • Babcock, M.S.1    Pednault, E.P.2    Olson, W.K.3
  • 5
    • 0020731864 scopus 로고
    • Rates of enzyme-catalyzed exchange determined by two-dimensional NMR; a study of glucose 6-phosphate anomerization and isomerization
    • Balaban, R. S. & Ferretti, J. A. (1983). Rates of enzyme-catalyzed exchange determined by two-dimensional NMR; a study of glucose 6-phosphate anomerization and isomerization. Proc. Natl Acad. Sci. USA, 80, 1241-1245.
    • (1983) Proc. Natl Acad. Sci. USA , vol.80 , pp. 1241-1245
    • Balaban, R.S.1    Ferretti, J.A.2
  • 6
    • 0026744912 scopus 로고
    • Preparation of isotopically labeled ribonucleotides for multidimensional NMR spectroscopy of RNA
    • Batey, R. T., Inada, M., Kujawinski, E., Puglisi, J. D. & Williamson, J. R. (1992). Preparation of isotopically labeled ribonucleotides for multidimensional NMR spectroscopy of RNA. Nucl. Acids Res. 20, 4515-4523.
    • (1992) Nucl. Acids Res. , vol.20 , pp. 4515-4523
    • Batey, R.T.1    Inada, M.2    Kujawinski, E.3    Puglisi, J.D.4    Williamson, J.R.5
  • 7
    • 0000452256 scopus 로고
    • Removal of F1 baseline distortion and optimization of folding in multidimensional NMR spectra
    • Bax, A., Ikura, M., Kay, L. E. & Zhu, G. (1991). Removal of F1 baseline distortion and optimization of folding in multidimensional NMR spectra. J. Magn. Reson. 91, 174-178.
    • (1991) J. Magn. Reson. , vol.91 , pp. 174-178
    • Bax, A.1    Ikura, M.2    Kay, L.E.3    Zhu, G.4
  • 9
    • 0030587890 scopus 로고    scopus 로고
    • Metal-binding sites in the major groove of a large ribozyme domain
    • Cate, J. H. & Doudna, J. A. (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.A.2
  • 12
  • 13
    • 0030587524 scopus 로고    scopus 로고
    • Structural evidence for specific S8-RNA and S8-protein interactions within the 30S ribosomal subunit; ribosomal protein S8 for Bacillus stearothermophilus at 1.9 Å resolution
    • Davies, C., Ramakrishnan, V. & White, S. W. (1996). Structural evidence for specific S8-RNA and S8-protein interactions within the 30S ribosomal subunit; ribosomal protein S8 for Bacillus stearothermophilus at 1.9 Å resolution. Structure, 4, 1093-1104.
    • (1996) Structure , vol.4 , pp. 1093-1104
    • Davies, C.1    Ramakrishnan, V.2    White, S.W.3
  • 14
    • 0019349494 scopus 로고
    • Escherichia coli ribosomal protein S8 feedback regulates part of Spc operon
    • Dean, D., Yeates, J. L. & Nomura, M. (1981). Escherichia coli ribosomal protein S8 feedback regulates part of Spc operon. Nature, 289, 89-91.
    • (1981) Nature , vol.289 , pp. 89-91
    • Dean, D.1    Yeates, J.L.2    Nomura, M.3
  • 15
    • 0031114540 scopus 로고    scopus 로고
    • Assignment methodology for larger RNA oligonucleotides; application to an ATP-binding RNA aptamer
    • Dieckmann, T. & Feigon, J. (1997). Assignment methodology for larger RNA oligonucleotides; application to an ATP-binding RNA aptamer. J. Biomol. NMR, 9, 259-272.
    • (1997) J. Biomol. NMR , vol.9 , pp. 259-272
    • Dieckmann, T.1    Feigon, J.2
  • 16
    • 0028869690 scopus 로고
    • Diversity of oligonucleotide function
    • (Richardson, C. C., Abelson, J. N., Meister, A. & Walsh, C. T., eds), Annual Reviews, Inc., Palo Alto, CA
    • Gold, L., Polisky, B., Uhlenbeck, O. & Yarus, M. (1995). Diversity of oligonucleotide function. In Annual Review of Biochemistry (Richardson, C. C., Abelson, J. N., Meister, A. & Walsh, C. T., eds), vol. 64, pp. 763-797, Annual Reviews, Inc., Palo Alto, CA.
    • (1995) Annual Review of Biochemistry , vol.64 , pp. 763-797
    • Gold, L.1    Polisky, B.2    Uhlenbeck, O.3    Yarus, M.4
  • 18
    • 0021610688 scopus 로고
    • Interaction of ribosomal proteins S6, S8, S15 and S18 with the central domain of 16 S ribosomal RNA from Escherichia coli
    • Gregory, R. J., Zeller, M. L., Thurlow, D. L., Gourse, R. L., Stark, M. J. R., Dahlberg, A. E. & Zimmermann, R. A. (1984). Interaction of ribosomal proteins S6, S8, S15 and S18 with the central domain of 16 S ribosomal RNA from Escherichia coli. J. Mol. Biol. 178, 287-302.
    • (1984) J. Mol. Biol. , vol.178 , pp. 287-302
    • Gregory, R.J.1    Zeller, M.L.2    Thurlow, D.L.3    Gourse, R.L.4    Stark, M.J.R.5    Dahlberg, A.E.6    Zimmermann, R.A.7
  • 19
    • 0024270439 scopus 로고
    • Interaction of Escherichia coli ribosomal protein S8 with its binding sites in ribosomal RNA and messenger RNA
    • Gregory, R. J., Cahill, P. B. F., Thurlow, D. L. & Zimmermann, R. A. (1988). Interaction of Escherichia coli ribosomal protein S8 with its binding sites in ribosomal RNA and messenger RNA. J. Mol. Biol. 204, 295-307.
    • (1988) J. Mol. Biol. , vol.204 , pp. 295-307
    • Gregory, R.J.1    Cahill, P.B.F.2    Thurlow, D.L.3    Zimmermann, R.A.4
  • 20
    • 0027265356 scopus 로고
    • Collection of small subunit (16 S and 16 S-like) ribosomal RNA structures
    • Gutell, R. R. (1993). Collection of small subunit (16 S and 16 S-like) ribosomal RNA structures. Nucl. Acids Res. 21, 3051-3054.
    • (1993) Nucl. Acids Res. , vol.21 , pp. 3051-3054
    • Gutell, R.R.1
  • 21
    • 0027390731 scopus 로고
    • Chemically modified RNA; approaches and applications
    • Heidenreich, O., Pieken, W. & Eckstein, F. (1993). Chemically modified RNA; approaches and applications. FASEB J. 7, 90-96.
    • (1993) FASEB J. , vol.7 , pp. 90-96
    • Heidenreich, O.1    Pieken, W.2    Eckstein, F.3
  • 22
    • 0016153699 scopus 로고
    • Assembly mapping of 30 S ribosomal proteins from Escherichia coli
    • Held, W. A., Ballou, B., Mizushima, S. & Nomura, M. (1974). Assembly mapping of 30 S ribosomal proteins from Escherichia coli. J. Biol. Chem. 249, 3103-3111.
    • (1974) J. Biol. Chem. , vol.249 , pp. 3103-3111
    • Held, W.A.1    Ballou, B.2    Mizushima, S.3    Nomura, M.4
  • 23
    • 48749149745 scopus 로고
    • Solvent suppression in Fourier transform nuclear magnetic resonance
    • Hore, P. J. (1983). Solvent suppression in Fourier transform nuclear magnetic resonance. J. Magn. Reson. 55, 283-300.
    • (1983) J. Magn. Reson. , vol.55 , pp. 283-300
    • Hore, P.J.1
  • 24
    • 0343359244 scopus 로고
    • Investigation of exchange processes by two-dimensional NMR spectroscopy
    • Jeener, J., Meier, B. H., Bachmann, P. & Ernst, R. R. (1979). Investigation of exchange processes by two-dimensional NMR spectroscopy. J. Chem. Phys. 71, 4546-4553.
    • (1979) J. Chem. Phys. , vol.71 , pp. 4546-4553
    • Jeener, J.1    Meier, B.H.2    Bachmann, P.3    Ernst, R.R.4
  • 25
    • 0030975691 scopus 로고    scopus 로고
    • Structural features of the binding site for ribosomal protein S8 in Escherichia coli 16 S rRNA defined using NMR spectroscopy
    • Kalurachchi, K., Uma, K., Zimmermann, R. A. & Nikonowicz, E. P. (1997). Structural features of the binding site for ribosomal protein S8 in Escherichia coli 16 S rRNA defined using NMR spectroscopy. Proc. Natl Acad. Sci. USA, 94, 2139-2144.
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 2139-2144
    • Kalurachchi, K.1    Uma, K.2    Zimmermann, R.A.3    Nikonowicz, E.P.4
  • 26
    • 44049117796 scopus 로고
    • Proton-detected hetero-TOCSY experiments with application to nucleic acids
    • Kellogg, G. W. (1992). Proton-detected hetero-TOCSY experiments with application to nucleic acids. J. Magn. Reson. 98, 176-182.
    • (1992) J. Magn. Reson. , vol.98 , pp. 176-182
    • Kellogg, G.W.1
  • 27
    • 0031570344 scopus 로고    scopus 로고
    • Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt (III) hexamine
    • Kieft, J. S. & Tinoco, I., Jr (1997). Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt (III) hexamine. Structure, 5, 713-721.
    • (1997) Structure , vol.5 , pp. 713-721
    • Kieft, J.S.1    Tinoco I., Jr.2
  • 28
    • 0021506622 scopus 로고
    • 15N enriched 5 S RNA fragment
    • 15N enriched 5 S RNA fragment. FEBS Letters, 175, 259-262.
    • (1984) FEBS Letters , vol.175 , pp. 259-262
    • Kime, M.J.1
  • 31
  • 33
    • 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. (1987). Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucl. Acids Res. 15, 8783-8789.
    • (1987) Nucl. Acids Res. , vol.15 , pp. 8783-8789
    • Milligan, J.F.1    Groebe, D.R.2    Witherell, G.W.3    Uhlenbeck, O.C.4
  • 34
    • 0031000077 scopus 로고    scopus 로고
    • The RNA binding site of S8 ribosomal protein of Escherichia coli; Selex and hydroxyl radical probing studies
    • Moine, H., Cachia, C., Westhof, E., Ehresmann, B. & Ehresmann, C. (1997). The RNA binding site of S8 ribosomal protein of Escherichia coli; Selex and hydroxyl radical probing studies. RNA, 3, 255-268.
    • (1997) RNA , vol.3 , pp. 255-268
    • Moine, H.1    Cachia, C.2    Westhof, E.3    Ehresmann, B.4    Ehresmann, C.5
  • 35
    • 0023053359 scopus 로고
    • Binding of Escherichia coli ribosomal protein S8 to 16S rRNA; kinetic and thermodynamic characterization
    • Mougel, M., Ehresmann, B. & Ehresmann, C. (1986). Binding of Escherichia coli ribosomal protein S8 to 16S rRNA; kinetic and thermodynamic characterization. Biochemistry, 25, 2756-2765.
    • (1986) Biochemistry , vol.25 , pp. 2756-2765
    • Mougel, M.1    Ehresmann, B.2    Ehresmann, C.3
  • 36
    • 0027203021 scopus 로고
    • Minimal 16S rRNA binding site and role of conserved nucleotides in Escherichia coli ribosomal protein S8 recognition
    • Mougel, M., Allmang, C., Eyermann, F., Cachia, C., Ehresmann, B. & Ehresmann, C. (1993). Minimal 16S rRNA binding site and role of conserved nucleotides in Escherichia coli ribosomal protein S8 recognition. Eur. J. Biochem. 215, 787-792.
    • (1993) Eur. J. Biochem. , vol.215 , pp. 787-792
    • Mougel, M.1    Allmang, C.2    Eyermann, F.3    Cachia, C.4    Ehresmann, B.5    Ehresmann, C.6
  • 39
    • 0003156250 scopus 로고
    • Divalent metal ions in RNA folding and catalysis
    • Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
    • Pan, T., Long, D. M. & Uhlenbeck, O. C. (1993). Divalent metal ions in RNA folding and catalysis. In The RNA World, pp. 271-285, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
    • (1993) The RNA World , pp. 271-285
    • Pan, T.1    Long, D.M.2    Uhlenbeck, O.C.3
  • 40
    • 0028885514 scopus 로고
    • Multidimensional heteronuclear NMR experiments for structure determination of isotopically labeled RNA
    • Pardi, A. (1995). Multidimensional heteronuclear NMR experiments for structure determination of isotopically labeled RNA. Methods Enzymol. 261, 350-380.
    • (1995) Methods Enzymol. , vol.261 , pp. 350-380
    • Pardi, A.1
  • 41
    • 0025762699 scopus 로고
    • Relationship between 2′-hydroxyls and magnesium binding in the hammerhead RNA domain; a model for ribozyme catalysis
    • Perreault, J. P., Labuda, D., Usman, N., Yang, J. H. & Cedergren, R. (1991). Relationship between 2′-hydroxyls and magnesium binding in the hammerhead RNA domain; a model for ribozyme catalysis. Biochemistry, 30, 4020-4025.
    • (1991) Biochemistry , vol.30 , pp. 4020-4025
    • Perreault, J.P.1    Labuda, D.2    Usman, N.3    Yang, J.H.4    Cedergren, R.5
  • 42
    • 0027398505 scopus 로고
    • Metal ion catalysis in the Tetrahymena ribozyme reaction
    • Piccirilli, J. A., Vyle, J. S., Caruthers, M. H. & Cech, T. R. (1993). Metal ion catalysis in the Tetrahymena ribozyme reaction. Nature, 361, 85-88.
    • (1993) Nature , vol.361 , pp. 85-88
    • Piccirilli, J.A.1    Vyle, J.S.2    Caruthers, M.H.3    Cech, T.R.4
  • 44
    • 0029932653 scopus 로고    scopus 로고
    • Neomycin, spermine and hexamminecobalt (III) share common structural motifs in converting B- To A-DNA
    • Robinson, H. & Wang, A. H. (1996). Neomycin, spermine and hexamminecobalt (III) share common structural motifs in converting B- to A-DNA. Nucl. Acids Res. 24, 676-682.
    • (1996) Nucl. Acids Res. , vol.24 , pp. 676-682
    • Robinson, H.1    Wang, A.H.2
  • 47
    • 0015463469 scopus 로고
    • Optimal conditions for the interaction of ribosomal protein S8 and 16S RNA and studies on the reaction mechanism
    • Schulte, C. & Garrett, R. A. (1972). Optimal conditions for the interaction of ribosomal protein S8 and 16S RNA and studies on the reaction mechanism. Mol. Gen. Genet. 119, 345-355.
    • (1972) Mol. Gen. Genet. , vol.119 , pp. 345-355
    • Schulte, C.1    Garrett, R.A.2
  • 48
    • 13444269041 scopus 로고
    • Computer-optimized decoupling scheme for wideband applications and low-level operation
    • Shaka, A. J., Barker, P. B. & Freeman, R. (1985). Computer-optimized decoupling scheme for wideband applications and low-level operation. J. Magn. Reson. 64, 547-552.
    • (1985) J. Magn. Reson. , vol.64 , pp. 547-552
    • Shaka, A.J.1    Barker, P.B.2    Freeman, R.3
  • 50
    • 0024292424 scopus 로고
    • Interaction of ribosomal proteins, S6, S8, S15 and S18 with the central domain of 16 S ribosomal RNA
    • Svensson, P., Changchien, L.-M., Craven, G. R. & Noller, H. F. (1988). Interaction of ribosomal proteins, S6, S8, S15 and S18 with the central domain of 16 S ribosomal RNA. J. Mol. Biol. 200, 301-308.
    • (1988) J. Mol. Biol. , vol.200 , pp. 301-308
    • Svensson, P.1    Changchien, L.-M.2    Craven, G.R.3    Noller, H.F.4
  • 51
    • 0001878781 scopus 로고
    • In vitro selection of functional RNA sequences
    • Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
    • Szostak, J. & Ellington, A. (1993). In vitro selection of functional RNA sequences. In The RNA World, pp. 511-534, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
    • (1993) The RNA World , pp. 511-534
    • Szostak, J.1    Ellington, A.2
  • 52
    • 0030940842 scopus 로고    scopus 로고
    • Identification and sequence analysis of contact sites between ribosomal proteins and rRNA in Escherichia coli 30S subunits by a new approach using matrix-assisted laser desorption/ionization-mass spectrometry combined with N-terminal microsequencing
    • Urlaub, H., Thiede, B., Müller, E.-C., Brimacombe, R. & Wittmann-Liebold, B. (1997). Identification and sequence analysis of contact sites between ribosomal proteins and rRNA in Escherichia coli 30S subunits by a new approach using matrix-assisted laser desorption/ionization-mass spectrometry combined with N-terminal microsequencing. J. Biol. Chem. 272, 14547-14555.
    • (1997) J. Biol. Chem. , vol.272 , pp. 14547-14555
    • Urlaub, H.1    Thiede, B.2    Müller, E.-C.3    Brimacombe, R.4    Wittmann-Liebold, B.5
  • 53
    • 0031213649 scopus 로고    scopus 로고
    • The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions
    • Välegard, K., Murray, J. B., Stonehouse, N. J., van den Worm, S., Stockley, P. G. & Lilijas, L. (1997). The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions. J. Mol. Biol. 270, 724-738.
    • (1997) J. Mol. Biol. , vol.270 , pp. 724-738
    • Välegard, K.1    Murray, J.B.2    Stonehouse, N.J.3    Van Den Worm, S.4    Stockley, P.G.5    Lilijas, L.6
  • 56
    • 0021100698 scopus 로고
    • The localization of multiple sites on 16S RNA which are cross-linked to proteins S7 and S8 in Escherichia coli 30S ribosomal subunits by treatment with 2-iminothiolane
    • Wower, I. & Brimacombe, R. (1983). The localization of multiple sites on 16S RNA which are cross-linked to proteins S7 and S8 in Escherichia coli 30S ribosomal subunits by treatment with 2-iminothiolane. Nucl. Acids Res. 11, 1419-1437.
    • (1983) Nucl. Acids Res. , vol.11 , pp. 1419-1437
    • Wower, I.1    Brimacombe, R.2
  • 57
    • 0026586406 scopus 로고
    • Mutagenesis of ribosomal protein S8 from Escherichia coli; defects in regulation of the spc operon
    • Wower, I., Kowaleski, M. P., Sears, L. E. & Zimmermann, R. A. (1992). Mutagenesis of ribosomal protein S8 from Escherichia coli; defects in regulation of the spc operon. J. Bacteriol. 174(4), 1213-1221.
    • (1992) J. Bacteriol. , vol.174 , Issue.4 , pp. 1213-1221
    • Wower, I.1    Kowaleski, M.P.2    Sears, L.E.3    Zimmermann, R.A.4
  • 58
    • 0028238892 scopus 로고
    • The binding site for ribosomal protein S8 in 16S rRNA and spc mRNA from Escherichia coli; minimum structural requirements and the effects of single bulged bases on S8-RNA interaction
    • Wu, H., Jiang, L. & Zimmermann, R. A. (1994). The binding site for ribosomal protein S8 in 16S rRNA and spc mRNA from Escherichia coli; minimum structural requirements and the effects of single bulged bases on S8-RNA interaction. Nucl. Acids Res. 22, 1687-1695.
    • (1994) Nucl. Acids Res. , vol.22 , pp. 1687-1695
    • Wu, H.1    Jiang, L.2    Zimmermann, R.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.