메뉴 건너뛰기




Volumn 274, Issue 1, 1997, Pages 101-113

The RNA binding domain of ribosomal protein L11: Three-dimensional structure of the RNA-bound form of the protein and its interaction with 23 S rRNA

Author keywords

23 S ribosomal RNA; Heteronuclear NMR; L11; Protein RNA; Ribosome

Indexed keywords

RIBOSOME PROTEIN; RNA; RNA 23S; RNA BINDING PROTEIN;

EID: 0030681341     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1379     Document Type: Article
Times cited : (48)

References (47)
  • 2
    • 44949286540 scopus 로고
    • Practical aspects of proton-carbon-carbon-proton three-dimensional correlation spectroscopy of 13C Labeled Proteins
    • Bax A., Clore G. M., Driscoll P. C., Gronenborn A. M., Ikura M., Kay L. E. Practical aspects of proton-carbon-carbon-proton three-dimensional correlation spectroscopy of 13C Labeled Proteins. J. Magn. Reson. 87:1990;620-627.
    • (1990) J. Magn. Reson. , vol.87 , pp. 620-627
    • Bax, A.1    Clore, G.M.2    Driscoll, P.C.3    Gronenborn, A.M.4    Ikura, M.5    Kay, L.E.6
  • 3
    • 0028544153 scopus 로고
    • Resonance assignment of methionine methyl groups and chi 3 angular information from long range proton-carbon and carbon-carbon J correlation in a calmodulin-peptide complex
    • Bax A., Delaglio F., Grzesiek S., Vuister G. W. Resonance assignment of methionine methyl groups and chi 3 angular information from long range proton-carbon and carbon-carbon J correlation in a calmodulin-peptide complex. J. Biomol. NMR. 4:1994;787-797.
    • (1994) J. Biomol. NMR , vol.4 , pp. 787-797
    • Bax, A.1    Delaglio, F.2    Grzesiek, S.3    Vuister, G.W.4
  • 5
    • 0027270989 scopus 로고
    • Co-crystal structure of the HNF-3/forkhead DNA-recognition motif resembles histone H5
    • Clark K. L., Halay E. D., Lai E., Burley S. K. Co-crystal structure of the HNF-3/forkhead DNA-recognition motif resembles histone H5. Nature. 364:1993;412-420.
    • (1993) Nature , vol.364 , pp. 412-420
    • Clark, K.L.1    Halay, E.D.2    Lai, E.3    Burley, S.K.4
  • 6
    • 0029044463 scopus 로고
    • Thermodynamics of RNA unfolding: Stabilization of ribosomal RNA tertiary structure by thiostrepton and ammonium ion
    • Draper D. E., Xing Y., Laing L. G. Thermodynamics of RNA unfolding: stabilization of ribosomal RNA tertiary structure by thiostrepton and ammonium ion. J. Mol. Biol. 249:1995;231-238.
    • (1995) J. Mol. Biol. , vol.249 , pp. 231-238
    • Draper, D.E.1    Xing, Y.2    Laing, L.G.3
  • 8
    • 0000711201 scopus 로고
    • Overcoming the ambiguity problem encountered in the analysis of nuclear Overhauser magnetic resonance spectra of symmetric dimer proteins
    • Folkers P. J. M., Folmer R. H. A., Konings R. N. H., Hilbers C. W. Overcoming the ambiguity problem encountered in the analysis of nuclear Overhauser magnetic resonance spectra of symmetric dimer proteins. J. Am. Chem. Soc. 115:1993;3798-3799.
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 3798-3799
    • Folkers, P.J.M.1    Folmer, R.H.A.2    Konings, R.N.H.3    Hilbers, C.W.4
  • 9
    • 0000041361 scopus 로고
    • A common sense approach to peak picking in two-, three-, and four-dimensional spectra using automatic computer analysis of contour diagrams
    • Garrett D. S., Powers R., Gronenborn A. M., Clore G. M. A common sense approach to peak picking in two-, three-, and four-dimensional spectra using automatic computer analysis of contour diagrams. J. Magn. Reson. 95:1991;214-220.
    • (1991) J. Magn. Reson. , vol.95 , pp. 214-220
    • Garrett, D.S.1    Powers, R.2    Gronenborn, A.M.3    Clore, G.M.4
  • 10
    • 9444245493 scopus 로고
    • Correlating backbone amide and side chain resonances in larger proteins by multiple relayed triple resonance NMR
    • Grzesiek S., Bax A. Correlating backbone amide and side chain resonances in larger proteins by multiple relayed triple resonance NMR. J. Am. Chem. Soc. 114:1992a;6291-6293.
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 6291-6293
    • Grzesiek, S.1    Bax, A.2
  • 11
    • 44049117010 scopus 로고
    • Improved 3D triple-resonance NMR techniques applied to a 31 kDa protein
    • Grzesiek S., Bax A. Improved 3D triple-resonance NMR techniques applied to a 31 kDa protein. J. Magn. Reson. 96:1992b;432-440.
    • (1992) J. Magn. Reson. , vol.96 , pp. 432-440
    • Grzesiek, S.1    Bax, A.2
  • 15
    • 0027366421 scopus 로고
    • NMR strategy for determining Xaa-Pro peptide bond configurations in proteins: Mutants of staphylococcal nuclease with altered configuration at proline-117
    • Hinck A. P., Eberhardt E. S., Markley J. L. NMR strategy for determining Xaa-Pro peptide bond configurations in proteins: mutants of staphylococcal nuclease with altered configuration at proline-117. Biochemistry. 32:1993;11810-11818.
    • (1993) Biochemistry , vol.32 , pp. 11810-11818
    • Hinck, A.P.1    Eberhardt, E.S.2    Markley, J.L.3
  • 16
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:1993;123-128.
    • (1993) J. Mol. Biol. , vol.233 , pp. 123-128
    • Holm, L.1    Sander, C.2
  • 17
    • 44049118502 scopus 로고
    • Pulse sequences for removal of the effects of cross correlation between dipolar and chemical-shift anisotropy relaxation mechanisms on the measurement of heteronuclear T 1 and T 2 values in proteins
    • Kay L. E., Nicholson L. K., Delaglio F., Bax A., Torchia D. A. Pulse sequences for removal of the effects of cross correlation between dipolar and chemical-shift anisotropy relaxation mechanisms on the measurement of heteronuclear T 1 and T 2 values in proteins. J. Magn. Reson. 97:1992;359-375.
    • (1992) J. Magn. Reson. , vol.97 , pp. 359-375
    • Kay, L.E.1    Nicholson, L.K.2    Delaglio, F.3    Bax, A.4    Torchia, D.A.5
  • 18
    • 0028200262 scopus 로고
    • Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules
    • Klemm J. D., Rould M. A., Aurora R., Herr W., Pabo C. O. Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules. Cell. 77:1994;21-32.
    • (1994) Cell , vol.77 , pp. 21-32
    • Klemm, J.D.1    Rould, M.A.2    Aurora, R.3    Herr, W.4    Pabo, C.O.5
  • 20
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
    • (1991) J. Appl. Crystallog. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 21
    • 0028234517 scopus 로고
    • Thermodynamics of RNA folding in a conserved ribosomal RNA domain
    • Laing L. G., Draper D. E. Thermodynamics of RNA folding in a conserved ribosomal RNA domain. J. Mol. Biol. 237:1994;560-576.
    • (1994) J. Mol. Biol. , vol.237 , pp. 560-576
    • Laing, L.G.1    Draper, D.E.2
  • 22
    • 0028237035 scopus 로고
    • Stabilization of RNA structure by magnesium ions
    • Laing L. G., Gluick T. C., Draper D. E. Stabilization of RNA structure by magnesium ions. J. Mol. Biol. 237:1994;577-587.
    • (1994) J. Mol. Biol. , vol.237 , pp. 577-587
    • Laing, L.G.1    Gluick, T.C.2    Draper, D.E.3
  • 23
    • 0000243829 scopus 로고
    • PROCHECK: A program to check the stereochemical quality of protein structures
    • Laskowski R. A., MacArthur M. W., Moss D. S., Thornton J. M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26:1993;283-291.
    • (1993) J. Appl. Crystallog. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 24
    • 0028828745 scopus 로고
    • Crystal structure of the MATa1/MATα2 homeodomain bound to DNA
    • Li T., Stark M. R., Johnson A. D., Wolberger C. Crystal structure of the MATa1/MATα2 homeodomain bound to DNA. Science. 270:1995;262-269.
    • (1995) Science , vol.270 , pp. 262-269
    • Li, T.1    Stark, M.R.2    Johnson, A.D.3    Wolberger, C.4
  • 25
    • 0028102703 scopus 로고
    • Bases defining ammonium and magnesium ion-dependent tertiary structure within the large subunit ribosomal RNA
    • Lu M., Draper D. E. Bases defining ammonium and magnesium ion-dependent tertiary structure within the large subunit ribosomal RNA. J. Mol. Biol. 244:1994;572-585.
    • (1994) J. Mol. Biol. , vol.244 , pp. 572-585
    • Lu, M.1    Draper, D.E.2
  • 26
    • 0031031915 scopus 로고    scopus 로고
    • High resolution solution structure of ribosomal protein L11-C76, a helical protein with a flexible loop that becomes structured upon binding to RNA
    • Markus M. A., Hinck A. P., Huang S., Draper D. E., Torchia D. A. High resolution solution structure of ribosomal protein L11-C76, a helical protein with a flexible loop that becomes structured upon binding to RNA. Nature Struct. Biol. 4:1997;70-77.
    • (1997) Nature Struct. Biol. , vol.4 , pp. 70-77
    • Markus, M.A.1    Hinck, A.P.2    Huang, S.3    Draper, D.E.4    Torchia, D.A.5
  • 27
    • 0026319199 scopus 로고
    • Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
    • Nicholls A., Sharp K. A., Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins: Struct. Funct. Genet. 11:1991;282-292.
    • (1991) Proteins: Struct. Funct. Genet. , vol.11 , pp. 282-292
    • Nicholls, A.1    Sharp, K.A.2    Honig, B.3
  • 28
    • 0029283884 scopus 로고
    • Chemical shifts and three-dimensional protein structures
    • Oldfield E. Chemical shifts and three-dimensional protein structures. J. Biomol. NMR. 5:1995;217-225.
    • (1995) J. Biomol. NMR , vol.5 , pp. 217-225
    • Oldfield, E.1
  • 29
    • 0024997404 scopus 로고
    • Protein-DNA contacts in the structure of a homeodomain-DNA complex determined by nuclear magnetic resonance spectroscopy in solution
    • Otting G., Qian Y. Q., Billeter M., Müller M., Affolter M., Gehring W. J., Wüthrich K. Protein-DNA contacts in the structure of a homeodomain-DNA complex determined by nuclear magnetic resonance spectroscopy in solution. EMBO J. 9:1990;3085-3092.
    • (1990) EMBO J. , vol.9 , pp. 3085-3092
    • Otting, G.1    Qian, Y.Q.2    Billeter, M.3    Müller, M.4    Affolter, M.5    Gehring, W.J.6    Wüthrich, K.7
  • 31
    • 0027732617 scopus 로고
    • Ribosomal proteins L11 and L10.(L12)4 and the antibiotic thiostrepton interact with overlapping regions of the 23 S rRNA backbone in the ribosomal GTPase center
    • Rosendahl G., Douthwaite S. Ribosomal proteins L11 and L10.(L12)4 and the antibiotic thiostrepton interact with overlapping regions of the 23 S rRNA backbone in the ribosomal GTPase center. J. Mol. Biol. 234:1993;1013-1020.
    • (1993) J. Mol. Biol. , vol.234 , pp. 1013-1020
    • Rosendahl, G.1    Douthwaite, S.2
  • 32
    • 0025807847 scopus 로고
    • Detection of a key tertiary interaction in the highly conserved GTPase center of large subunit ribosomal RNA
    • Ryan P. C., Draper D. E. Detection of a key tertiary interaction in the highly conserved GTPase center of large subunit ribosomal RNA. Proc. Natl Acad. Sci. USA. 88:1991;6308-6312.
    • (1991) Proc. Natl Acad. Sci. USA , vol.88 , pp. 6308-6312
    • Ryan, P.C.1    Draper, D.E.2
  • 33
    • 0025999688 scopus 로고
    • Recognition of the highly conserved GTPase center of 23 S ribosomal RNA by ribosomal protein L11 and the antibiotic thiostrepton
    • Ryan P. C., Lu M., Draper D. E. Recognition of the highly conserved GTPase center of 23 S ribosomal RNA by ribosomal protein L11 and the antibiotic thiostrepton. J. Mol. Biol. 221:1991;1257-1268.
    • (1991) J. Mol. Biol. , vol.221 , pp. 1257-1268
    • Ryan, P.C.1    Lu, M.2    Draper, D.E.3
  • 34
    • 0019810825 scopus 로고
    • The binding site for ribosomal protein L11 within 23 S ribosomal RNA of Escherichia coli
    • Schmidt F. J., Thompson J., Lee K., Dijk J., Cundliffe E. The binding site for ribosomal protein L11 within 23 S ribosomal RNA of Escherichia coli. J. Biol. Chem. 256:1981;12301-12305.
    • (1981) J. Biol. Chem. , vol.256 , pp. 12301-12305
    • Schmidt, F.J.1    Thompson, J.2    Lee, K.3    Dijk, J.4    Cundliffe, E.5
  • 35
    • 0018572602 scopus 로고
    • On the biological role of ribosomal protein BM-L11 of Bacillus megaterium, homologous with Escherichia coli ribosomal protein L11
    • Stark M., Cundliffe E. On the biological role of ribosomal protein BM-L11 of Bacillus megaterium, homologous with Escherichia coli ribosomal protein L11. J. Mol. Biol. 134:1979;767-779.
    • (1979) J. Mol. Biol. , vol.134 , pp. 767-779
    • Stark, M.1    Cundliffe, E.2
  • 36
    • 0000838671 scopus 로고
    • Estimation of interatomic distances in proteins from NOE spectra at longer mixing times using an empirical two-spin equation
    • Suri A. K., Levy R. M. Estimation of interatomic distances in proteins from NOE spectra at longer mixing times using an empirical two-spin equation. J. Magn. Reson. ser. B. 101:1993;320-324.
    • (1993) J. Magn. Reson. Ser. B , vol.101 , pp. 320-324
    • Suri, A.K.1    Levy, R.M.2
  • 37
    • 0029205592 scopus 로고
    • A relaxation-matrix analysis of distance-constraint ranges for NOEs in proteins at long mixing times
    • Suri A. K., Levy R. M. A relaxation-matrix analysis of distance-constraint ranges for NOEs in proteins at long mixing times. J. Magn. Reson. ser. B. 106:1995;24-31.
    • (1995) J. Magn. Reson. Ser. B , vol.106 , pp. 24-31
    • Suri, A.K.1    Levy, R.M.2
  • 38
    • 0021287182 scopus 로고
    • 2-terminal domain of Escherichia coli ribosomal protein L11. Its three-dimensional location and its role in the binding of release factors 1 and 2
    • 2-terminal domain of Escherichia coli ribosomal protein L11. Its three-dimensional location and its role in the binding of release factors 1 and 2. J. Biol. Chem. 259:1984;7317-7324.
    • (1984) J. Biol. Chem. , vol.259 , pp. 7317-7324
    • Tate, W.P.1    Dognin, M.J.2    Noah, M.3    Stöffler-Meilicke, M.4    Stöffler, G.5
  • 39
    • 0018497597 scopus 로고
    • Binding of thiostrepton to a complex of 23 S rRNA with ribosomal protein L11
    • Thompson J., Cundliffe E., Stark M. Binding of thiostrepton to a complex of 23 S rRNA with ribosomal protein L11. Eur. J. Biochem. 98:1979;261-265.
    • (1979) Eur. J. Biochem. , vol.98 , pp. 261-265
    • Thompson, J.1    Cundliffe, E.2    Stark, M.3
  • 43
    • 0001501991 scopus 로고
    • 15N-enriched human ubiquitin
    • 15N-enriched human ubiquitin. J. Am. Chem. Soc. 117:1995;1810-1813.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 1810-1813
    • Wang, A.C.1    Bax, A.2
  • 44
    • 0027374419 scopus 로고
    • Specific ammonium ion requirement for functional ribosomal RNA tertiary structure
    • Wang Y.-X., Lu M., Draper D. E. Specific ammonium ion requirement for functional ribosomal RNA tertiary structure. Biochemistry. 32:1993;12279-12282.
    • (1993) Biochemistry , vol.32 , pp. 12279-12282
    • Wang, Y.-X.1    Lu, M.2    Draper, D.E.3
  • 45
    • 0028393784 scopus 로고
    • 13C Chemical-shift index: A simple method for the identification of protein secondary structure using 13C chemical shift data
    • 13C Chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical shift data. J. Biomol. NMR. 4:1994;171-180.
    • (1994) J. Biomol. NMR , vol.4 , pp. 171-180
    • Wishart, D.S.1    Sykes, B.D.2
  • 46
    • 0030020855 scopus 로고    scopus 로고
    • Cooperative interactions of RNA and thiostrepton antibiotic with two domains of ribosomal protein L11
    • Xing Y., Draper D. E. Cooperative interactions of RNA and thiostrepton antibiotic with two domains of ribosomal protein L11. Biochemistry. 35:1996;1581-1588.
    • (1996) Biochemistry , vol.35 , pp. 1581-1588
    • Xing, Y.1    Draper, D.E.2
  • 47
    • 0031024655 scopus 로고    scopus 로고
    • The RNA binding domain of ribosomal protein L11 is structurally similar to homeodomains
    • Xing Y., GuhaThakurta D., Draper D. E. The RNA binding domain of ribosomal protein L11 is structurally similar to homeodomains. Nature Struct. Biol. 4:1997;24-27.
    • (1997) Nature Struct. Biol. , vol.4 , pp. 24-27
    • Xing, Y.1    Guhathakurta, D.2    Draper, D.E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.