Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

High resolution solution structure of ribosomal protein L11-C76, a helical protein with a flexible loop that becomes structured upon binding to RNA

Nature Structural Biology volume 4, pages 70–77 (1997)Cite this article

Abstract

The structure of the C-terminal RNA recognition domain of ribosomal protein L11 has been solved by heteronuclear three-dimensional nuclear magnetic resonance spectroscopy. Although the structure can be considered high resolution in the core, 15 residues between helix α1 and strand β1 form an extended, unstructured loop. 15N transverse relaxation measurements suggest that the loop is moving on a picosecond-to-nanosecond time scale in the free protein but not in the protein bound to RNA. Chemical shifts differences between the free protein and the bound protein suggest that the loop as well as the C-terminal end of helix α3 are involved in RNA binding.

Access through your institution
Buy or subscribe

This is a preview of subscription content, access via your institution

Access options

Access through your institution

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Similar content being viewed by others

References

  1. 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, 767–779 (1979).

    Article  CAS  Google Scholar 

  2. Thompson, J., Cundliffe, E. & Stark, M. Binding of Thiostrepton to a Complex of 23-S rRNA with Ribosomal Protein L11. Eur. J. Biochem. 98, 261–265 (1979).

    Article  CAS  Google Scholar 

  3. Egebjerg, J., Douthwaite, S. & Garrett, R.A. Antibiotic interactions at the GTPase-associated centre within Escherichia coli 23S rRNA. EMBO J. 8, 607–611 (1989).

    Article  CAS  Google Scholar 

  4. Pucciarelli, M.G., Remacha, M., Vilella, M.D. & Ballesta, J.P.G. The 26S rRNA binding ribosomal protein equivalent to bacterial protein L11 is encoded by unspliced duplicated genes in Saccccharomyces cerevisiae. Nucleic Acids Res. 18, 4409–4416 (1990).

    Article  CAS  Google Scholar 

  5. Liljas, A. Comparative biochemistry and biophysics of ribosomal proteins. Int. Rev. Cytol. 124, 103–136 (1991).

    Article  CAS  Google Scholar 

  6. 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, 12301–12305 (1981).

    CAS  PubMed  Google Scholar 

  7. 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, 1257–1268 (1991).

    Article  CAS  Google Scholar 

  8. 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 centre. J. Mol. Biol. 234, 1013–1020 (1993).

    Article  CAS  Google Scholar 

  9. Xing, Y. & Draper, D.E. Stabilization of a ribosomal RNA tertiary structure by ribosomal protein L11. J. Mol. Biol. 249, 319–331 (1995).

    Article  CAS  Google Scholar 

  10. Cundliffe, E. Involvement of specific portions of ribosomal RNA in defined ribosomal functions: a study utilizing antibiotics. in Structure, Function, and Genetics of Ribosomes (eds B. Hardesty and G. Kramer) 586–604 (Springer-Verlag, New York, 1986).

    Chapter  Google Scholar 

  11. Xing, Y. & Draper, D.E. Cooperative interactions of RNA and thiostrepton antibiotic with two domains of ribosomal protein L11. Biochemistry 35, 1581–1588 (1996).

    Article  CAS  Google Scholar 

  12. Howarth, O.W. & Lilley, D.M. Carbon-13-NMR of peptides and proteins. Prog. NMR Spect. 12, 1–40 (1978).

    Article  CAS  Google Scholar 

  13. Richardson, J.S. & Richardson, D.C. Amino acid preferences for specific locations at the ends of α helices. Science 240, 1648–1652 (1988).

    Article  CAS  Google Scholar 

  14. Wagner, G. NMR relaxation and protein mobility. Curr. Opin. Struct. Biol. 3, 748–754 (1993).

    Article  CAS  Google Scholar 

  15. Golden, B.L., Ramakrishnan, V. & White, S.W. Ribosomal protein L6: structural evidence of gene duplication from a primitive RNA binding protein. EMBO Jour. 12, 4901–4908 (1993).

    Article  CAS  Google Scholar 

  16. Leijonmarck, M. & Liljas, A. Structure of the C-terminal domain of the ribosomal protein L7/L12 from Escherichia coli at 1.7 Å. J. Mol. Biol. 195, 555–580 (1987).

    Article  CAS  Google Scholar 

  17. Wilson, K.S., Appelt, K., Badger, J., Tanaka, I. & White, S.W. Crystal structure of a prokaryotic ribosomal protein. Proc. Natl. Acad. Sci. USA 83, 7251–7255 (1986).

    Article  CAS  Google Scholar 

  18. Ramakrishnan, V. & White, S.W. The structure of ribosomal protein S5 reveals sites of interaction with 16S RNA. Nature 358, 768–771 (1992).

    Article  CAS  Google Scholar 

  19. Jaishree, T.N., Ramakrishnan, V. & White, S.W. Solution structure of prokaryotic ribosomal protein 517 by high-resolution NMR spectroscopy. Biochemistry 35, 2845–2853 (1996).

    Article  CAS  Google Scholar 

  20. Mattaj, I.W. & Nagai, K. Recruiting proteins to the RNA world. Nature Struct. Biol. 2, 518–522 (1995).

    Article  CAS  Google Scholar 

  21. Tan, R., Chen, L., Buettner, J.A., Hudson, D. & Frankel, A.D. RNA recognition by an isolated α helix. Cell 73, 1031–1040 (1993).

    Article  CAS  Google Scholar 

  22. Xing, Y, GuhaThakurta, D. & Draper, D.E. [TITLE] Nature Struct. Biol. 4, xxx–xxx (1997)

    Google Scholar 

  23. Qian, Y.Q. et al. The structure of the Antennapedia homeodomain determined by NMR spectroscopy in solution: comparison with prokaryotic repressers. Cell 59, 573–580 (1989).

    Article  CAS  Google Scholar 

  24. Kissinger, C.R., Liu, B., Martin-Blanco, E., Kornberg, T.B. & Pabo, C.O. Crystal structure of an engrailed homeodomain-DNA complex at 2.8 Å resolution: A framework for understanding homeodomain-DNA interactions. Cell 63, 579–590 (1990).

    Article  CAS  Google Scholar 

  25. Gitti, R.K. et al. Structure of the amino-terminal core domain of the HIV-1 capsid protein. Science 273, 231–235 (1996).

    Article  CAS  Google Scholar 

  26. Oubridge, C., Ito, N., Evans, P.R., Teo, C.-H. & Nagai, K. Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature 372, 432–438 (1994).

    Article  CAS  Google Scholar 

  27. Allain, F.H.-T. et al. Specificity of ribonucleoprotein interaction determined by RNA folding during complex formation. Nature 380, 646–650 (1996).

    Article  CAS  Google Scholar 

  28. Puglisi, J.D., Chen, L., Blanchard, S. & Frankel, A.D. Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex. Science 270, 1200–1203 (1995).

    Article  CAS  Google Scholar 

  29. Studier, F.W., Rosenberg, A.H., Dunn, J.J. & Dubendorff, J.W. Use of T7 RNA polymerase to direct expression of cloned genes. Meths Enzymol. 185, 60–89 (1990).

    Article  CAS  Google Scholar 

  30. Lu, M. & Draper, D.E. Bases defining an ammonium and magnesium ion-dependent tertiary structure within the large subunit ribosomal RNA. J. Mol. Biol. 244, 572–585 (1994).

    Article  CAS  Google Scholar 

  31. Laing, L.G. & Draper, D.E. Thermodynamics of RNA folding in a conserved ribosomal RNA domain. J. Mol. Biol. 237, 560–576 (1994).

    Article  CAS  Google Scholar 

  32. Delaglio, F. et al. NMR pipe: A multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277–293 (1995).

    Article  CAS  Google Scholar 

  33. 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, 214–220 (1991).

    CAS  Google Scholar 

  34. Bodenhausen, G. & Ruben, D.J. Natural abundance nitrogen-15 NMR by enhanced heteronuclear spectroscopy. Chem. Phys. Lett. 69, 185–189 (1980).

    Article  CAS  Google Scholar 

  35. Piotto, M., Saudek, V. & Sklenar, V. Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. J. Biomol. NMR 2, 661–665 (1992).

    Article  CAS  Google Scholar 

  36. Grzesiek, S. & Bax, A. The importance of not saturating H2O in protein NMR. application to sensitivity enhancement and NOE measurements. J. Am. Chem. Soc. 115, 12593–12594 (1993).

    Article  CAS  Google Scholar 

  37. Vuister, G.W. & Bax, A. Resolution enhancement and spectral editing of uniformly 13C-Enriched proteins by homonuclear broadband 13C decoupling. J. Magn. Reson. 98, 428–435 (1992).

    CAS  Google Scholar 

  38. Wittekind, M. & Mueller, L. HNCACB, a high-sensitivity 3D NMR experiment to correlate amide-proton and nitrogen resonances with the alpha- and beta-carbon resonances in proteins. J. Magn. Reson. B 101, 201–205 (1993).

    Article  CAS  Google Scholar 

  39. 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, 6291–6293 (1992).

    Article  CAS  Google Scholar 

  40. Kay, L.E., Ikura, M., Tschudin, R. & Bax, A. Three-dimensional triple-resonance spectroscopy of isotopically enriched proteins. J. Magn. Reson. 89, 496–514 (1990).

    CAS  Google Scholar 

  41. Grzesiek, S., Anglister, J. & Bax, A. Correlation of backbone amide and aliphatic side-chain resonances in 13C/15N-enriched proteins by isotropic mixing of 13C magnetization. J. Magn. Reson. B 101, 114–119 (1993).

    Article  CAS  Google Scholar 

  42. Bax, A., Core, G.M. & Gronenborn, A.M. 1H-1H Correlation via isotropic mixing of 13C magnetization, a new three-dimensional approach for assigning 1H and 13C spectra of 13C-enriched proteins. J. Magn. Reson. 88, 425–431 (1990).

    CAS  Google Scholar 

  43. Bax, A., Delaglio, F., Grzesiek, S. & Vuister, G.W. Resonance assignments of methionine methyl groups and χ3 angular information from long-range proton-carbon and carbon-carbon J correlation in a calmodulin-peptide complex. J. Biomol. NMR 4, 787–797 (1994).

    Article  CAS  Google Scholar 

  44. Vuister, G.W. & Bax, A. Quantitative J correlation: A new approach for measuring homonuclear three-bond J(HN-Hα) coupling constants in 15N-enriched proteins. J. Am. Chem. Soc. 115, 7772–7777 (1993).

    Article  CAS  Google Scholar 

  45. Archer, S.J., Ikura, M., Torchia, D.A. & Bax, A. An alternative 3D NMR technique for correlating backbone 15N with side chain Hβ resonances in larger proteins. J. Magn. Reson. 95, 636–641 (1991).

    CAS  Google Scholar 

  46. Grzesiek, S., Kuboniwa, H., Hinck, A.P. & Bax, A. Multiple-quantum line narrowing for measurement of Hα-HβJ coupling in isotopically enriched proteins. J. Am. Chem. Soc. 117, 5312–5315 (1995).

    Article  CAS  Google Scholar 

  47. Grzesiek, S., Vuister, G.W. & Bax, A. A simple and sensitive experiment for measurement of JCC couplings between backbone carbonyl and methyl carbons in isotopically enriched proteins. J. Biomol. NMR 3, 487–493 (1993).

    CAS  PubMed  Google Scholar 

  48. Vuister, G.W., Wang, A.C. & Bax, A. Measurement of three-bond nitrogen-carbon J couplings in proteins uniformly enriched in 15N and 13C. J. Am. Chem. Soc. 115, 5334–5335 (1993).

    Article  CAS  Google Scholar 

  49. Bax, A., Max, D. & Zax, D. Measurement of long-range 13C-13C J couplings in a 20-kDa protein-peptide complex. J. Am. Chem. Soc. 114, 6923–6925 (1992).

    Article  CAS  Google Scholar 

  50. Vuister, G.W. & Bax, A. Measurement of two- and three-bond proton to methyl-carbon J couplings in proteins uniformly enriched with 13C. J. Magn. Reson. B 102, 228–231 (1993).

    Article  CAS  Google Scholar 

  51. Brünger, A.T. X-PLOR Version 3.1. A System for X-ray Crystallography and NMR (Yale University Press, New Haven, 1992).

    Google Scholar 

  52. Kay, L.E., Torchia, D.A. & Bax, A. Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease. Biochemistry 28, 8972–8979 (1989).

    Article  CAS  Google Scholar 

  53. 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 in the measurement of heteronuclear T1 and T2 values in proteins. J. Magn. Reson. 97, 359–375 (1992).

    CAS  Google Scholar 

  54. Kraulis, P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946–950 (1991).

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Molecular Structural Biology Unit, National Institute of Dental Research, 30 Convent Drive, Bethesda, Maryland, 20892-4320, USA

    Michelle A. Markus, Andrew P. Hinck, Shengrong Huang & Dennis A. Torchia

  2. Department of Chemistry, Johns Hopkins University, Baltimore, Maryland, 21218, USA

    Shengrong Huang & David E. Draper

Authors
  1. Michelle A. Markus
    View author publications

    Search author on:PubMed Google Scholar

  2. Andrew P. Hinck
    View author publications

    Search author on:PubMed Google Scholar

  3. Shengrong Huang
    View author publications

    Search author on:PubMed Google Scholar

  4. David E. Draper
    View author publications

    Search author on:PubMed Google Scholar

  5. Dennis A. Torchia
    View author publications

    Search author on:PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Markus, M., Hinck, A., Huang, S. et al. High resolution solution structure of ribosomal protein L11-C76, a helical protein with a flexible loop that becomes structured upon binding to RNA. Nat Struct Mol Biol 4, 70–77 (1997). https://doi.org/10.1038/nsb0197-70

Download citation

  • Received:

  • Accepted:

  • Issue date:

  • DOI: https://doi.org/10.1038/nsb0197-70

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing