Ribosome-associated factor Y adopts a fold resembling a double-stranded RNA binding domain scaffold

European Journal of Biochemistry

Volumn 269, Issue 21, 2002, Pages 5182-5191

  Ye, Keqiong ^a   Serganov, Alexander ^a   Hu, Weidong ^a   Garber, Maria ^b   Patel, Dinshaw J ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b INSTITUTE OF PROTEIN RESEARCH   (Russian Federation)

Author keywords

Backbone dynamics; dsRBD; Molecular alignment; Residual dipolar couplings; RNA binding domain

Indexed keywords

BACTERIAL PROTEIN; DOUBLE STRANDED RNA;

ARTICLE; BETA SHEET; BINDING SITE; CARBON NUCLEAR MAGNETIC RESONANCE; CARBOXY TERMINAL SEQUENCE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; MASS SPECTROMETRY; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; RIBOSOME SUBUNIT; RNA BINDING; TIME;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BINDING SITES; COMPUTER SIMULATION; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MASS SPECTROMETRY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; RIBOSOMAL PROTEINS; RNA, DOUBLE-STRANDED; RNA-BINDING PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; SPINACIA OLERACEA; STRUCTURE-ACTIVITY RELATIONSHIP; XENOPUS PROTEINS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; MUS;

EID: 0036431442     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1432-1033.2002.03222.x     Document Type: Article

References (49)

1. Agafonov, D.E., Kolb, V.A., Nazimov, I.V. & Spirin, A.S. (1999) A protein residing at the subunit interface of the bacterial ribo-some. Proc. Natl Acad. Sci. USA 96, 12345-12349.
2. Agafonov, D.E., Kolb, V.A. & Spirin, A.S. (2001) Ribosome-associated protein that inhibits translation at the aminoacyl-tRNA binding stage. EMBO Rep. 2, 399-402.
3. Maki, Y., Yoshida, H. & Wada, A. (2000) Two proteins, YfiA and YhbH, associated with resting ribosomes in stationary phase Escherichia coli. Genes Cells 5, 965-974.
4. 54-dependent promoters. Mol. Microbiol. 3, 1765-1775.
5. Schmidt, J., Srinivasa, B., Weglohner, W. & Subramanian, A.R. (1993) A small novel chloroplast ribosomal protein (S31) that has no apparent counterpart in the E. coli ribosome. Biochem. Mol. Biol. Int. 29, 25-31.
6. Zhou, D.X. & Mache, R. (1989) Presence in the stroma of chloroplasts of a large pool of a ribosomal protein not structurally related to any Escherichia coli ribosomal protein. Mol. Gen. Genet. 219, 204-208.
7. Johnson, C.H., Kruft, V. & Subramanian, A.R. (1990) Identification of a plastid-specific ribosomal protein in the 30S subunit of chloroplast ribosomes and isolation of the cDNA clone encoding its cytoplasmic precursor. J. Biol. Chem. 265, 12790-12795.
8. Bubunenko, M.G. & Subramanian, A.R. (1994) Recognition of novel and divergent higher plant chloroplast ribosomal proteins by Escherichia coli ribosome during in vivo assembly. J. Biol. Chem. 269, 18223-18231.
9. Tan, X., Varughese, M. & Widger, W.R. (1994) A light-repressed transcript found in Synechococcus PCC 7002 is similar to a chloroplast-specific small subunit ribosomal protein and to a transcription modulator protein associated with sigma 54. J. Biol. Chem. 269, 20905-20912.
10. Parsons, L., Eisenstein, E. & Orban, J. (2001) Solution structure of HI0257, a bacterial ribosome binding protein. Biochemistry 40, 10979-10986.
11. 13C-enriched fusion proteins in Escherichia coli. J. Biomol. NMR 7, 131-141.
12. Johnson, B.A. & Blevins, R.A. (1994) NMRView: A computer program for the visualization and analysis of NMR data. J. Biomol. NMR 4, 603-614.
13. Bax, A. & Grzesiek, S. (1993) Methodological advances in protein NMR. Acc. Chem. Res. 26, 131-138.
14. 13 C labeling. Biochemistry 28, 7510-7516.
15. 15N-enriched proteins. J. Am. Chem. Soc. 115, 7772-7777.
16. Garrett,D.S.,Kuszewski,J.,Hancock,T.J.,Lodi,P.J.,Vuister,G.W., Gronenborn, A.M. & Clore, G.M. (1994) The impact of direct refinement against three-bond HN-CαH coupling constants on protein structure determination by NMR. J. Magn. Reson. B. 104, 99-103.
17. Nilges, M., Macias, M.J., O'Donoghue, S.I. & Oschkinat, H. (1997) Automated NOESY interpretation with ambiguous distance restraints: The refined NMR solution structure of the pleckstrin homology domain from beta-spectrin. J. Mol. Biol. 269, 408-422.
18. Hansen, M.R., Mueller, L. & Pardi, A. (1998) Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions. Nat. Struct. Biol. 5, 1065-1074.
19. CH splittings from magnetic-field dependence of J modulation in two-dimensional NMR spectra. J. Magn. Reson. 124, 512-515.
20. Losonczi, J.A., Andrec, M., Fischer, M.W.F. & Prestegard, J.M. (1999) Order matrix analysis of residual dipolar coupling using singular value decomposition. J. Magn. Reson. 138, 334-342.
21. Tjandra, N. & Bax, A. (1997) Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science 278, 1111-1114.
22. Clore, G.M., Gronenborn, A.M. & Bax, A. (1998) A robust method for determining the magnitude of the fully asymmetric alignment tensor of oriented macromolecules in the absence of structural information. J. Magn. Reson. 133, 216-221.
23. Bai, Y., Milne, J.S., Mayne, L. & Englander, S.W. (1993) Primary structure effects on peptide group hydrogen exchange. Proteins 17, 75-86.
24. 15N NMR relaxation. Biochemistry 33, 5984-6003.
25. Brünger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S. et al. (1998) Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905-921.
26. Fletcher, C.M., Jones, D.N.M., Diamond, R. & Neuhaus, D. (1996) Treatment of NOE constraints involving equivalent or nonstereoassigned protons in calculations of biomacromolecular structures. J. Biomol. NMR 8, 292-310.
27. Koradi, R., Billeter, M. & Wüthrich, K. (1996) MOLMOL: A program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51-55.
28. 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.
29. Studier, F.W., Rosenberg, A.H., Dunn, J.J. & Dubendorff, J.W. (1990) Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol. 185, 60-89.
30. Prestegard, J.H., al-Hashimi, H.M. & Tolman, J.R. (2000) NMR structures of biomolecules using field oriented media and residual dipolar couplings. Q. Rev. Biophys. 33, 371-424.
31. Zweckstetter, M. & Bax, A. (2000) Prediction of sterically induced alignment in a dilute liquid crystalline phase: Aid to protein structure determination by NMR. J. Am. Chem. Soc. 122, 3791-3792.
32. Feher, V.A. & Cavanagh, J. (1999) Millisecond-timescale motions contribute to the function of the bacterial response regulator protein Spo0F. Nature 400, 289-293.
33. Nanduri, S., Rahman, F., Williams, B.R. & Qin, J. (2000) A dynamically tuned double-stranded RNA binding mechanism for the activation of antiviral kinase PKR. EMBO J. 19, 5567-5574.
34. Pearson,W.R.&Lipman,D.J.(1988)Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA 85, 2444-2448.
35. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
36. Parkhill, J., Dougan, G., James, K.D., Thomson, N.R., Pickard, D., Wain, J., Churcher, C., Mungall, K.L., Bentley, S.D., Holden, M.T. et al. (2001) Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 413, 848-852.
37. McClelland, M., Sanderson, K.E., Spieth, J., Clifton, S.W., Latreille, P., Courtney, L., Porwollik, S., Ali, J., Dante, M., Du, F. et al. (2001) Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413, 852-856.
38. Parkhill, J., Wren, B.W., Thomson, N.R., Titball, R.W., Holden, M.T., Prentice, M.B., Sebaihia, M., James, K.D., Churcher, C., Mungall, K.L. et al. (2001) Genome sequence of Yersinia pestis, the causative agent of plague. Nature 413, 523-527.
39. May, B.J., Zhang, Q., Li, L.L., Paustian, M.L., Whittam, T.S. & Kapur, V. (2001) Complete genomic sequence of Pasteurella multocida, Pm70. Proc. Natl Acad. Sci. USA 98, 3460-3465.
40. Murzin, A.G., Brenner, S.E., Hubbard, T. & Chothia, C. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
41. Sander, C. & Schneider, R. (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9, 56-68.
42. Ryter, J.M. & Schultz, S.C. (1998) Molecular basis of double-stranded RNA-protein interactions: Structure of a dsRNA-binding domain complexed with dsRNA. EMBO J. 17, 7505-7513.
43. Nanduri, S., Carpick, B.W., Yang, Y., Williams, B.R. & Qin, J. (1998) Structure of the double-stranded RNA-binding domain of the protein kinase PKR reveals the molecular basis of its dsRNA-mediated activation. EMBO J. 17, 5458-5465.
44. Ramos, A., Grunert, S., Adams, J., Micklem, D.R., Proctor, M.R., Freund, S., Bycroft, M., St. Johnston, D. & Varani, G. (2000) RNA recognition by a Staufen double-stranded RNA-binding domain. EMBO J. 19, 997-1009.
45. St Johnston, D., Brown, N.H., Gall, J.G. & Jantsch, M. (1992) A conserved double-stranded RNA-binding domain. Proc. Natl Acad. Sci. USA 89, 10979-10983.
46. Sankaranarayanan, R., Dock-Bregeon, A.C., Romby, P., Caillet, J., Springer, M., Rees, B., Ehresmann, C., Ehresmann, B. & Moras, D. (1999) The structure of threonyl-tRNA synthetase-tRNA (Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site. Cell 97, 371-381.
47. Bycroft, M., Grunert, S., Murzin, A.G., Proctor, M. & St John-ston, D. (1995) NMR solution structure of a dsRNA binding domain from Drosophila staufen protein reveals homology to the N-terminal domain of ribosomal protein S5. EMBO J. 14, 3563-3571.
48. Laskowski, R.A., Rullmannn, J.A., MacArthur, M.W., Kaptein, R. & Thornton, J.M. (1996) AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8, 477-486.
49. Holm, L. & Sander, C. (1996) Mapping the protein universe. Science 273, 595-603.