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. 1998 Aug 17;17(16):4559–4571. doi: 10.1093/emboj/17.16.4559

The solution structure of ribosomal protein S4 delta41 reveals two subdomains and a positively charged surface that may interact with RNA.

M A Markus 1, R B Gerstner 1, D E Draper 1, D A Torchia 1
PMCID: PMC1170786  PMID: 9707416

Abstract

S4 is one of the first proteins to bind to 16S RNA during assembly of the prokaryotic ribosome. Residues 43-200 of S4 from Bacillus stearothermophilus (S4 Delta41) bind specifically to both 16S rRNA and to a pseudoknot within the alpha operon mRNA. As a first step toward understanding how S4 recognizes and organizes RNA, we have solved the structure of S4 Delta41 in solution by multidimensional heteronuclear nuclear magnetic resonance spectroscopy. The fold consists of two globular subdomains, one comprised of four helices and the other comprised of a five-stranded antiparallel beta-sheet and three helices. Although cross-linking studies suggest that residues between helices alpha2 and alpha3 are close to RNA, the concentration of positive charge along the crevice between the two subdomains suggests that this could be an RNA-binding site. In contrast to the L11 RNA-binding domain studied previously, S4 Delta41 shows no fast local motions, suggesting that it has less capacity for refolding to fit RNA. The independently determined crystal structure of S4 Delta41 shows similar features, although there is small rotation of the subdomains compared with the solution structure. The relative orientation of the subdomains in solution will be verified with further study.

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Selected References

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  1. Allen P. N., Noller H. F. Mutations in ribosomal proteins S4 and S12 influence the higher order structure of 16 S ribosomal RNA. J Mol Biol. 1989 Aug 5;208(3):457–468. doi: 10.1016/0022-2836(89)90509-3. [DOI] [PubMed] [Google Scholar]
  2. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  3. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389–3402. doi: 10.1093/nar/25.17.3389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Baker A. M., Draper D. E. Messenger RNA recognition by fragments of ribosomal protein S4. J Biol Chem. 1995 Sep 29;270(39):22939–22945. doi: 10.1074/jbc.270.39.22939. [DOI] [PubMed] [Google Scholar]
  5. Bax A., Tjandra N. High-resolution heteronuclear NMR of human ubiquitin in an aqueous liquid crystalline medium. J Biomol NMR. 1997 Oct;10(3):289–292. doi: 10.1023/a:1018308717741. [DOI] [PubMed] [Google Scholar]
  6. Deckman I. C., Draper D. E. S4-alpha mRNA translation regulation complex. II. Secondary structures of the RNA regulatory site in the presence and absence of S4. J Mol Biol. 1987 Jul 20;196(2):323–332. doi: 10.1016/0022-2836(87)90693-0. [DOI] [PubMed] [Google Scholar]
  7. Deckman I. C., Draper D. E. Specific interaction between ribosomal protein S4 and the alpha operon messenger RNA. Biochemistry. 1985 Dec 31;24(27):7860–7865. doi: 10.1021/bi00348a002. [DOI] [PubMed] [Google Scholar]
  8. Deckman I. C., Draper D. E., Thomas M. S. S4-alpha mRNA translation repression complex. I. Thermodynamics of formation. J Mol Biol. 1987 Jul 20;196(2):313–322. doi: 10.1016/0022-2836(87)90692-9. [DOI] [PubMed] [Google Scholar]
  9. Delaglio F., Grzesiek S., Vuister G. W., Zhu G., Pfeifer J., Bax A. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR. 1995 Nov;6(3):277–293. doi: 10.1007/BF00197809. [DOI] [PubMed] [Google Scholar]
  10. Dodd J., Hill W. E. Physical characteristics of ribosomal protein S4 from Escherichia coli. J Biol Chem. 1987 Feb 25;262(6):2478–2484. [PubMed] [Google Scholar]
  11. Gill S. C., von Hippel P. H. Calculation of protein extinction coefficients from amino acid sequence data. Anal Biochem. 1989 Nov 1;182(2):319–326. doi: 10.1016/0003-2697(89)90602-7. [DOI] [PubMed] [Google Scholar]
  12. Grzesiek S., Bax A. Amino acid type determination in the sequential assignment procedure of uniformly 13C/15N-enriched proteins. J Biomol NMR. 1993 Mar;3(2):185–204. doi: 10.1007/BF00178261. [DOI] [PubMed] [Google Scholar]
  13. Hinck A. P., Markus M. A., Huang S., Grzesiek S., Kustonovich I., Draper D. E., Torchia D. A. 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. J Mol Biol. 1997 Nov 21;274(1):101–113. doi: 10.1006/jmbi.1997.1379. [DOI] [PubMed] [Google Scholar]
  14. Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol. 1993 Sep 5;233(1):123–138. doi: 10.1006/jmbi.1993.1489. [DOI] [PubMed] [Google Scholar]
  15. Kisker C., Hinrichs W., Tovar K., Hillen W., Saenger W. The complex formed between Tet repressor and tetracycline-Mg2+ reveals mechanism of antibiotic resistance. J Mol Biol. 1995 Mar 24;247(2):260–280. doi: 10.1006/jmbi.1994.0138. [DOI] [PubMed] [Google Scholar]
  16. Kodandapani R., Pio F., Ni C. Z., Piccialli G., Klemsz M., McKercher S., Maki R. A., Ely K. R. A new pattern for helix-turn-helix recognition revealed by the PU.1 ETS-domain-DNA complex. Nature. 1996 Apr 4;380(6573):456–460. doi: 10.1038/380456a0. [DOI] [PubMed] [Google Scholar]
  17. Kuboniwa H., Grzesiek S., Delaglio F., Bax A. Measurement of HN-H alpha J couplings in calcium-free calmodulin using new 2D and 3D water-flip-back methods. J Biomol NMR. 1994 Nov;4(6):871–878. doi: 10.1007/BF00398416. [DOI] [PubMed] [Google Scholar]
  18. Liebman S. W., Chernoff Y. O., Liu R. The accuracy center of a eukaryotic ribosome. Biochem Cell Biol. 1995 Nov-Dec;73(11-12):1141–1149. doi: 10.1139/o95-123. [DOI] [PubMed] [Google Scholar]
  19. Malhotra A., Severinova E., Darst S. A. Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase. Cell. 1996 Oct 4;87(1):127–136. doi: 10.1016/s0092-8674(00)81329-x. [DOI] [PubMed] [Google Scholar]
  20. 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. Nat Struct Biol. 1997 Jan;4(1):70–77. doi: 10.1038/nsb0197-70. [DOI] [PubMed] [Google Scholar]
  21. Neri D., Szyperski T., Otting G., Senn H., Wüthrich K. Stereospecific nuclear magnetic resonance assignments of the methyl groups of valine and leucine in the DNA-binding domain of the 434 repressor by biosynthetically directed fractional 13C labeling. Biochemistry. 1989 Sep 19;28(19):7510–7516. doi: 10.1021/bi00445a003. [DOI] [PubMed] [Google Scholar]
  22. Nicholls A., Sharp K. A., Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins. 1991;11(4):281–296. doi: 10.1002/prot.340110407. [DOI] [PubMed] [Google Scholar]
  23. Nowotny V., Nierhaus K. H. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051–7055. doi: 10.1021/bi00418a057. [DOI] [PubMed] [Google Scholar]
  24. Sapag A., Vartikar J. V., Draper D. E. Dissection of the 16S rRNA binding site for ribosomal protein S4. Biochim Biophys Acta. 1990 Aug 27;1050(1-3):34–37. doi: 10.1016/0167-4781(90)90137-q. [DOI] [PubMed] [Google Scholar]
  25. Studier F. W., Rosenberg A. H., Dunn J. J., Dubendorff J. W. Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol. 1990;185:60–89. doi: 10.1016/0076-6879(90)85008-c. [DOI] [PubMed] [Google Scholar]
  26. Tjandra N., Bax A. Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science. 1997 Nov 7;278(5340):1111–1114. doi: 10.1126/science.278.5340.1111. [DOI] [PubMed] [Google Scholar]
  27. Urlaub H., Kruft V., Bischof O., Müller E. C., Wittmann-Liebold B. Protein-rRNA binding features and their structural and functional implications in ribosomes as determined by cross-linking studies. EMBO J. 1995 Sep 15;14(18):4578–4588. doi: 10.1002/j.1460-2075.1995.tb00137.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Vartikar J. V., Draper D. E. S4-16 S ribosomal RNA complex. Binding constant measurements and specific recognition of a 460-nucleotide region. J Mol Biol. 1989 Sep 20;209(2):221–234. doi: 10.1016/0022-2836(89)90274-x. [DOI] [PubMed] [Google Scholar]
  29. Wagner G. Prospects for NMR of large proteins. J Biomol NMR. 1993 Jul;3(4):375–385. doi: 10.1007/BF00176005. [DOI] [PubMed] [Google Scholar]
  30. Wishart D. S., Sykes B. D. The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data. J Biomol NMR. 1994 Mar;4(2):171–180. doi: 10.1007/BF00175245. [DOI] [PubMed] [Google Scholar]

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