The crystal structure of ribosomal protein L14 reveals an important organizational component of the translational apparatus

Structure

Volumn 4, Issue 1, 1996, Pages 55-66

  Davies, Christopher ^a   White, Stephen W ^a   Ramakrishnan, V ^b,c  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

^b BROOKHAVEN NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

Author keywords

Multiwavelength anomalous dispersion (MAD); Ribosomal protein L14; Ribosomes; X ray crystallography

Indexed keywords

GEOBACILLUS STEAROTHERMOPHILUS;

RIBOSOMAL PROTEIN L14; RIBOSOME PROTEIN; RNA 23S; RNA BINDING PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; GEOBACILLUS STEAROTHERMOPHILUS; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PROTEIN BINDING; PROTEIN SECONDARY STRUCTURE; PROTEIN SYNTHESIS; RIBOSOME; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; BACILLUS STEAROTHERMOPHILUS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; EVOLUTION, MOLECULAR; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN BIOSYNTHESIS; PROTEIN STRUCTURE, SECONDARY; RIBOSOMAL PROTEINS; RIBOSOMES; RNA, RIBOSOMAL, 23S; RNA-BINDING PROTEINS;

EID: 0029643859     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(96)00009-3     Document Type: Article

References (67)

1. Holmes, K.C. (1994). Solving the structures of macromolecular complexes. Structure 2, 589-593.
2. Frank, J., et al., & Agrawal, R.K. (1995). A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome. Nature, 376, 441-444.
3. Stark, H., et al., & van Heel, M. (1995). The 70S Escherichia coli ribosome at 23 Å resolution: fitting the ribosomal RNA. Structure 3, 815-821.
4. Ramakrishnan, V. & Gerchman, S.E. (1991). Cloning, sequencing and overexpression of genes for ribosomal protein from Bacillus stearothermophilus. J. Biol. Chem. 266, 880-885.
5. Ramakrishnan, V. & White, S.W. (1992). The structure of ribosomal protein S5 reveals sites of interaction with 16S rRNA. Nature 358, 768-771.
6. 15N NMR. Biochemistry 32, 12812-12820.
7. Golden, B.L., Ramakrishnan, V. & White, S.W. (1993). Ribosomal protein L6: structural evidence of gene duplication from a primitive RNA binding protein. EMBO J. 12, 4901-4908.
8. Hoffman, D.W., et al., & Ramakrishnan, V. (1994). Crystal structure of prokaryotic ribosomal protein L9: a bi-lobed RNA-binding protein. EMBO J. 13, 205-212.
9. Lindahl, M., et al., & Amons, R. (1994). Crystal structure of the ribosomal protein S6 from Thermus thermophilus. EMBO J. 13, 1249-1254.
10. Nikonov. S., et al., & Liljas, A. (1995). Crystal structure of the RNA-binding ribosomal protein L1 from Thermus thermophilus. EMBO J., in press.
11. Noller, H.F., Hoffarth, V. & Zimniak, L. (1992). Unusual resistance of peptidyl transferase to protein extraction procedures. Science 256, 1416-1419.
12. Purohit, P. & Stern, S. (1994). Interactions of a small RNA with antibiotic and RNA ligands of the 30S subunit. Nature 370, 659-662.
13. Wool, I.G., Chan, Y-L. & Glück, A. (1995). The structure and the evolution of mammalian ribosomal proteins. Biochem. Cell Biol., in press.
14. Herold, M. & Nierhaus, K.N. (1987), Incorporation of six additional proteins to complete the assembly map of the 50S subunit from Escherichia coli ribosomes. J. Biol. Chem. 262, 8826-8833.
15. Walleczek, J., Schüler, D., Stöffler-Meilicke, M., Brimacombe, R. & Stöffler, G. (1988). A model for the spatial arrangement of the proteins in the large subunit of the Escherichia coli ribosome. EMBO J. 7, 3571-3576.
16. Noller, H.F., et al., & Weiser, B. (1996). Structure and function of ribosomal RNA. Biochem. Cell Biol., in press.
17. Davies, C., Gerchman, S.E., Kycia, J.H., McGee, K., Ramakrishnan, V. & White, S.W. (1994). Crystallization and preliminary X-ray diffraction studies of bacterial ribosomal protein L14. Acta Cryst. D 50, 790-792.
18. Hendrickson, W.A. (1991). Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science 254, 51-58.
19. Ramakrishnan, V., Finch, J.T., Gravaziano, C., Lee, P.L. & Sweet, R.M. (1993). Crystal structure of globular domain of histone H5 and its implications for nucleosome binding. Nature 362, 219-223.
20. Levitt, M. & Chothia, C. (1976). Structural patterns in globular proteins. Nature 261, 552-558.
21. McLachlan, A.D. (1979). Gene duplication in the structural evolution of chymotrypsin. J. Mol. Biol. 128, 49-79.
22. Rould, M.A., Perona, J.J., Söll, D. & Steitz, T.A. (1989). Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 Å resolution. Science 246, 1135-1142.
23. Asp. Science 252, 1682-1689.
24. Ser. Science 263, 1404-1410.
25. Oubridge. C., Ito, N., Evans, P.R., Teo, C.-H. & Nagai, K. (1994). 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.
26. Herbst, K.L., Nichols, L.M., Gesteland, R.F. & Weiss, R.B. (1994). A mutation in ribosomal protein L9 affects ribosomal hopping during translation of gene 60 from bacteriophage T4. Proc. Natl. Acad. Sci. USA 91, 12525-12529.
27. Urlaub, H., Kruft, V., Bischof, O., Mueller, E.C. & Wittmann-Liebold, B. (1995). Protein-rRNA binding features and their structural and functional implications in ribosomes as determined by cross-linking studies. EMBO J. 14, 4578-4588.
28. Traut, R.R., Tewari, D.S., Sommer, A., Gavino, G.R., Olson, H.M. & Glitz. D.G. (1986). Protein topography of ribosomal functional domains: effects of monoclonal antibodies to different epitopes in Escherichia coli protein L7/L12 on ribosome function and structure. In Structure, Function and Genetics of Ribosomes. (Hardesty, B. and Kramer, G., eds), pp. 286-308, Springer-Verlag, NY.
29. Walleczek, J., Martin, T., Redl, B., Stöffler-Meilicke, M. & Stöffler, G. (1989). Comparative cross-linking study on the 50S ribosomal subunit from Escherichia coli. Biochemistry 28, 4099-4105.
30. Walleczek, J., Redl, B., Stöffler-Meilicke, M. & Stöffler, G. (1989). Protein-protein cross-linking of the 50S ribosomal subunit of Escherichia coli using 2-iminothiolane. J. Biol. Chem. 264, 4231-4237.
31. Hunt, J.F., Weaver, A.J., Landry, S., Gierasch, L & Deisenhofer, J. (1996). The crystal structure of the GroES co-chaperonin at 2.8 Å resolution. Nature 379, 37-45.
32. Bernabeu. C., Conde, P., Vazquez, D. & Ballesta, J.P. (1979). Peptidyl transferase of bacterial ribosome: resistance to proteinase K. Eur. J. Biochem. 93, 527-533.
33. Hummel, H., Piepersburg, W. & Bock, A. (1979). Analysis of lincomycin mutations in Escherichia coli. Mol. Gen. Genet. 169, 345-347.
34. Monro, R.E. & Vazquez, D. (1967). Ribosome-catalysed peptidyl transfer: effects of some inhibitors of protein synthesis. J. Mol. Biol. 28, 161-165.
35. Oßwald, M., Greuer, B. & Brimacombe R. (1990). Localization of a series of RNA-protein cross-link sites in the 23S and 5S ribosomal RNA from Escherichia coli, induced by treatment of 50S subunits with three different bifunctional reagents. Nucleic Acids Res. 18, 6755-6760.
36. Graifer, D.M., Babkina, G.T., Matasova, N.B., Vladimirov, S.N., Karpova, G.G. & Vlassov, V.V. (1989). Structural arrangement of tRNA binding sites on Escherichia coli ribosomes, as revealed from data on affinity labelling with photoactivatable tRNA derivatives. Biochem. Biophys. Acta 1008, 146-156.
37. Vladimirov, S.N., Graifer, D.M., Karpova, G.G., Semenkov, Y.P., Makhno, V.I. & Kirillov, S.V. (1985). The effect of GTP hydrolysis and transpeptidation on the arrangement of aminoacyl-tRNA at the A-site of Escherichia coli 70S ribosomes. FEBS lett. 181, 367-372.
38. Sköld, S.E. (1982). Chemical cross-linking of elongation factor G to both subunits of the 70S ribosomes from Escherichia coli. Eur. J. Biochem. 127, 225-229.
39. Traut, R.R., Lambert, J.M. & Kenny, J.W. (1983). Ribosomal proteins L7/L12 cross-link to proteins in separate regions of the 50S ribosomal subunit of Escherichia coli. J. Biol. Chem. 258, 14592-14598.
40. Wilson, K.S., Appelt, K., Badger, J., Tanaka, I. & White, S.W. (1986). Crystal structure of a prokaryotic ribosomal protein. Proc. Natl. Acad. Sci. USA 83, 7251-7255.
41. Leijonmarck, M., Eriksson, S. & Liljas, A. (1980). Crystal structure of a ribosomal component at 2.6 Å resolution. Nature 286, 824-826.
42. Czworkowski, J., Wang, J., Steitz, T.A. & Moore, P.B. (1994). The crystal structure of elongation factor G complexed with GDP, at 2.7 Å resolution. EMBO J. 13, 3661-3668.
43. Ævarsson, A., et al., & Liljas, A. (1994). Three-dimensional structure of the ribosomal translocase: elongation factor G from Thermus thermophilus. EMBO J. 13, 3669-3677.
44. Hoffman, D.W., Query, C.C., Golden, B.L., White, S.W. & Keene, J.K. (1991). RNA-binding domain of the A protein component of the U1 small nuclear ribonucleoprotein analyzed by NMR spectroscopy is structurally similar to ribosomal proteins. Proc. Natl. Acad. Sci. USA 88, 2495-2499.
45. Nagai, K., Oubridge, C., Jessen, T.H., Li J. & Evans, P.R. (1990). Crystal structure of the RNA-binding domain of the U1 small nuclear ribonucleoprotein A. Nature 348, 515-520.
46. Murzin, A.G. (1993). OB (oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. EMBO J. 12, 861-867.
47. Hendrickson, W.A., Smith, J.L., Phizackerley, R.P. & Merritt, E.A. (1988). Crystallographic analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation. Proteins 4, 77-88.
48. Leslie, A.G.W. (1992). Recent changes to the MOSFLM package for processing film and image plate data. CCP4 ESF-EACMB Newsl. Protein Crystallogr. No. 26. SERC Daresbury Laboratory, Warrington, UK.
49. Collaborative Computational Project, Number 4. (1994). The CCP4 suite: programs for protein crystallography Acta Cryst. D 50, 760-763.
50. Furey, W. & Swaminathan, S. (1996). PHASES-95: A program package for the processing and analysis of diffraction data from macromolecules. Methods Enzymol., in press.
51. Biou, V., Shu, F. & Ramakrishnan, V. (1995). X-ray crystallography shows that translational initiation factor IF3 consists of two compact α/β domains linked by an α-helix. EMBO J. 14, 4056-4064.
52. Jones, T.A. (1985). Diffraction methods for biological macromolecules: Interactive computer graphics: FRODO. Methods Enzymol. 115, 157-171.
53. Brünger, A.T., Kuriyan, J. & Karplus, M. (1987). Crystallographic R-factor refinement by molecular dynamics. J. Mol. Biol. 203, 803-816.
54. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283-291.
55. Luthy, R., Bowie, J.U. & Eisenberg, D. (1992). Assessment of protein models with 3-dimensional profiles. Nature 356, 83-85.
56. Jones, T.A., Zou, J.-Y., Cowan, S.W. & Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst. A 47, 110-119.
57. Kraulis, P.J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946-950.
58. Kimura, M., Kimura, J. & Ashman, K. (1985). The complete primary structure of ribosomal proteins L1, L14, L15, L23, L24 and L29 from Bacillus stearothermophilus. Eur. J. Biochem. 150, 491-497.
59. Kimura, M. & Wittmann-Liebold, B. (1982). Primary structure of protein L14 from Escherichía coli ribosomes. Biochem. Int. 4, 567-574.
60. Zhou, D.X., Quigley, F., Massenet, O. & Mache, R. (1989). Co-transcription of the S10- and spc-like operons in spinach chloroplasts and identification of three of their gene products. Mol. Gen. Genet. 216, 439-445.
61. Lou, J.K., Cruz, F.D. & Wu, M. (1989). Nucleotide sequence of the chloroplast ribosomal protein gene L14 in Chlamydomonas reinhardtii. Nucleic Acids Res. 17, 3587.
62. Arndt, E. (1990). Nucleotide sequence of four genes encoding ribosomal proteins from the 'S10 and spectinomycin' operon equivalent region in the archaebacterium Halobacterium marismortui. FEBS Lett. 267, 193-198.
63. Auer, J., Spicker, G. & Boeck, A. (1989). Organization and structure of the Methanococcus transcriptional unit homologous to the Escherichia coli "spectinomycin operon". Implications for the evolutionary relationship of 70S and 80S ribosomes. J. Mol. Biol. 209, 21-36.
64. Leer, R.J., van Raamsdonk-Duin, M.M., Hagendoorn, M.J., Mager, W.H. & Planta, R.J. (1984). Structural comparison of yeast ribosomal protein genes. Nucleic Acids Res. 12, 6685-6700.
65. Herault, Y., Michael, D., Chatelain, G. & Brun, G. (1991). cDNA and predicted amino acid sequences of the human ribosomal protein genes rpS12 and rpL17. Nucleic Acids Res. 19, 4001.
66. Chan, Y.L., Paz, V. & Wool, I.G. (1991). The primary structure of rat ribosomal protein L23. Biochem. Biophys. Res. Commun. 178, 1153-1159.
67. Nicholls, A., Sharp, K.A. & Honig, B. (1991). Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281-296.