Solution structure of the ribosomal protein S19 from Thermus thermophilus

Journal of Molecular Biology

Volumn 292, Issue 5, 1999, Pages 1071-1081

  Helgstrand, Magnus ^a   Rak, Alexey V ^b   Allard, Peter ^a   Davydova, Natalia ^b   Garber, Maria B ^b   Härd, Torleif ^a  

^a ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^b INSTITUTE OF PROTEIN RESEARCH   (Russian Federation)

Author keywords

NMR spectroscopy; Protein structure; Ribosome; Thermus thermophilus; Translation

Indexed keywords

BACTERIAL PROTEIN; RIBOSOMAL PROTEIN S19; RIBOSOME PROTEIN; RIBOSOME RNA; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CARBON NUCLEAR MAGNETIC RESONANCE; CONTROLLED STUDY; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROKARYOTE; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; RNA TRANSLATION; THERMUS THERMOPHILUS;

BACTERIA (MICROORGANISMS); PROKARYOTA; THERMUS THERMOPHILUS;

EID: 0033536672     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3122     Document Type: Article

References (39)

1. Agrawal R. K., Frank J. Structural studies of the translational apparatus. Curr. Opin. Struct. Biol. 9:1999;215-221.
2. Ban N., Freeborn B., Nissen P., Penczek P., Grassucci R. A., Sweet R., Frank J., Moore P. B., Steitz T. A. A 9 Å resolution X-ray crystallographic map of the large ribosomal subunit. Cell. 93:1998;1105-1115.
3. 13C-enriched proteins. J. Magn. Reson. 88:1990;425-431.
4. Brünger A. T. X-PLOR Version 3.1. A system for X-ray Crystallography and NMR. 1992;Yale University Press, New Haven.
5. Brünger A. T., Clore G. M., Gronenborn A. M., Karplus M. Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin. Proc. Natl Acad. Sci. USA. 83:1986;3801-3805.
6. Buck M. A., Cooperman B. S. Single protein omission reconstitution studies of tetracycline binding to the 30 S subunit of Escherichia coli ribosomes. Biochemistry. 29:1990;5374-5379.
7. Capel M. S., Engelman D. M., Freeborn B. R., Kjeldgaard M., Langer J. A., Ramakrishnan V., Schindler D. G., Schneider D. K., Schoenborn B. P., Sillers I.-Y., Yabuki S., Moore P. B. A complete mapping of the proteins in the small ribosomal subunit of Escherichia coli. Science. 238:1987;1403-1406.
8. Davydova N. L., Rak A. V., Gryaznova O. I., Liljas A., Jonsson B.-H., Berglund H., Härd T., Garber M. B. Preliminary NMR studies of Thermus thermophilus ribosomal protein S19 overproduced in Escherichia coli. FEBS Letters. 415:1997;155-159.
9. Edison A. S., Abildgaard F., Westler W. M., Mooberry E. S., Markley J. L. Practical introduction to theory and implementation of multinuclear, multidimensional nuclear magnetic resonance experiments. Methods Enzymol. 239:1994;3-79.
10. 15N NMR relaxation. Biochemistry. 33:1994;5984-6003.
11. Fletcher C. M., Jones D. N. M., Diamond R., Neuhaus D. Treatment of NOE constraints involving equivalent or nonstereoassigned protons in calculations of biomacromolecular structures. J. Biomol. NMR. 8:1996;292-310.
12. 1H spin system identification in macromolecules. J. Am. Chem. Soc. 110:1988;7870-7872.
13. 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.
14. Grzesiek S., Bax A. An efficient experiment for sequential backbone assignment of medium-sized isotopically enriched proteins. J. Magn. Reson. 99:1992b;201-207.
15. 13C magnetization. J. Magn. Reson. ser. B. 101:1993;114-119.
16. Haaf A., LeClaire L. III, Roberts G., Kent H. M., Roberts T. M., Stewart M., Neuhaus D. Solution structure of the motile major sperm protein (MSP) of Ascaris suum - evidence for two manganese binding sites and the possible role of divalent cations in filament formation. J. Mol. Biol. 284:1998;1611-1624.
17. Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:1993;123-138.
18. 15N spectra of larger proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin. Biochemistry. 29:1990;4659-4667.
19. Jeffrey G. A., Saenger W. Hydrogen Bonding in Biological Structures. 1991;Springer-Verlag, Berlin.
20. Kay L. E., Keifer P., Saarinen T. Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity. J. Am. Chem. Soc. 114:1992;10663-10665.
21. Kjaer M., Andersen K. V., Poulsen F. M. Automated and semiautomated analysis of homo- and heteronuclear multidimensional nuclear magnetic resonance spectra of proteins: the program Pronto. Methods Enzymol. 239:1994;288-307.
22. Koradi R., Billeter M., Wüthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14:1996;51-55.
23. 15N-separated NOE data. A novel real-space ab initio approach. J. Mol. Biol. 243:1994;696-718.
24. αJ couplings in calcium-free calmodulin using new 2D and 3D water-flip-back methods. J. Biomol. NMR. 4:1994;871-878.
25. Laskowski R. A., Rullmann J. A. C., MacArthur M. W., Kaptein R., Thornton J. M. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR. 8:1996;477-486.
26. Lu G. A WWW service system for automatic comparison of protein structures. Protein Data Bank Quarterly Newsletter. 78:1996;10-11.
27. Ludvigsen S., Poulsen F. M. Positive φ-angles in proteins by nuclear magnetic resonance spectroscopy. J. Biomol. NMR. 2:1992;227-233.
28. Macura S., Ernst R. R. Elucidation of cross relaxation in liquids by two-dimensional N.M.R. spectroscopy. Mol. Phys. 41:1980;95-117.
29. Mizushima S., Nomura M. Assembly mapping of 30 S ribosomal proteins from E. coli. Nature. 226:1970;1214-1218.
30. Nicholls A., Honig B. A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Bolzmann equation. J. Comput. Chem. 12:1990;435-445.
31. Pohl T., Wittmann-Liebold B. Identification of a cross-link in the Escherichia coli ribosomal protein pair S13-S19 at the amino acid level. J. Biol. Chem. 263:1988;4293-4301.
32. Powers T., Noller H. F. Hydroxyl radical footprinting of ribosomal proteins on 16 S rRNA. RNA. 1:1995;194-209.
33. Powers T., Changchien L.-M., Craven G. R., Noller H. F. Probing the assembly of the 3′ major domain of 16 S ribosomal RNA. Quaternary interactions involving ribosomal proteins S7, S9 and S19. J. Mol. Biol. 200:1988;309-319.
34. Ramakrishnan V., White S. W. Ribosomal protein structures: insights into the architecture, machinery and evolution of the ribosome. Trends Biochem. Sci. 23:1998;208-212.
35. Wishart D. S., Sykes B. D. Chemical shifts as a tool for structure determination. Methods Enzymol. 239:1994;363-392.
36. Wüthrich K. NMR of Proteins and Nucleic Acids. 1986;John Wiley & Sons, New York.
37. 13C-labeled proteins via scalar couplings. J. Am. Chem. Soc. 115:1993;11054-11055.
38. 2H labeled proteins with high sensitivity. J. Am. Chem. Soc. 116:1994;11655-11666.
39. 15N resonance assignments of the N-terminal SH3 domain of drk in folded and unfolded states using enhanced-sensitivity pulsed field gradient NMR techniques. J. Biomol. NMR. 4:1994;845-858.