Selection of tRNA by the ribosome requires a transition from an open to a closed form

Cell

Volumn 111, Issue 5, 2002, Pages 721-732

  Ogle, James M ^a   Murphy IV, Frank V ^a   Tarry, Michael J ^a   Ramakrishnan, V ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PAROMOMYCIN; TRANSFER RNA;

ANTICODON; ARTICLE; BINDING AFFINITY; CODON; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; GEOMETRY; HYDROGEN BOND; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; RIBOSOME; RIBOSOME SUBUNIT; SOLVATION;

EID: 0037184536     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(02)01086-3     Document Type: Article

References (51)

1. Bartlett P.A., Marlowe C.K. Evaluation of intrinsic binding energy from a hydrogen bonding group in an enzyme inhibitor. Science. 235:1987;569-571.
2. Battle D.J., Doudna J.A. Specificity of RNA-RNA helix recognition. Proc. Natl. Acad. Sci. USA. 99:2002;11676-11681.
3. 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. Crystallography & NMR system. a new software suite for macromolecular structure determination Acta Crystallogr. D54:1998;905-921.
4. Carter A.P., Clemons W.M.J., Brodersen D.E., Morgan-Warren R.J., Wimberly B.T., Ramakrishnan V. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature. 407:2000;340-348.
5. Cheetham G.M., Steitz T.A. Insights into transcription. structure and function of single-subunit DNA-dependent RNA polymerases Curr. Opin. Struct. Biol. 10:2000;117-123.
6. Chen X., McDowell J.A., Kierzek R., Krugh T.R., Turner D.H. Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for G.U. pairs. Biochemistry. 39:2000;8970-8982.
7. Clemons W.M.J., May J.L., Wimberly B.T., McCutcheon J.P., Capel M.S., Ramakrishnan V. Structure of a bacterial 30S ribosomal subunit at 5.5 A resolution. Nature. 400:1999;833-840.
8. CCP4 The CCP4 (Collaborative Computational Project 4) suite. programs for protein crystallography Acta Crystallogr. D50:1994;760-763.
9. Clemons W.M. Jr., Brodersen D.E., McCutcheon J.P., May J.L., Carter A.P., Morgan-Warren R.J., Wimberly B.T., Ramakrishnan V. Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus. purification, crystallization and structure determination J. Mol. Biol. 310:2001;827-843.
10. Crick F.H.C. Codon-anticodon pairing. the wobble hypothesis J. Mol. Biol. 19:1966;548-555.
11. Davies J., Gilbert W., Gorini L. Streptomycin, suppression, and the code. Proc. Natl. Acad. Sci. USA. 51:1964;883-890.
12. Doherty E.A., Batey R.T., Masquida B., Doudna J.A. A universal mode of helix packing in RNA. Nat. Struct. Biol. 8:2001;339-343.
13. Eisinger J., Feuer B., Yamane T. Codon-anticodon binding in tRNAphe. Nat. New Biol. 231:1971;126-128.
14. Fourmy D., Recht M.I., Blanchard S.C., Puglisi J.D. Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Science. 274:1996;1367-1371.
15. Glukhova M.A., Belitsina N.V., Spirin A.S. A study of codon-dependent binding of aminoacyl-tRNA with the ribosomal 30-S subparticle of Escherichia coli. Determination of the active-particle fraction and binding constants in different media. Eur. J. Biochem. 52:1975;197-202.
16. Grosjean H.J., de Henau S., Crothers D.M. On the physical basis for ambiguity in genetic coding interactions. Proc. Natl. Acad. Sci. USA. 75:1978;610-614.
17. Herschlag D. The role of induced fit and conformational changes in specificity and catalysis. Bioorg. Chem. 16:1988;62-96.
18. Hopfield J.J. Kinetic proofreading. a new mechanism for reducing errors in biosynthetic processes requiring high specificity Proc. Natl. Acad. Sci. USA. 71:1974;4135-4139.
19. Jones T.A., Kjeldgaard M. Electron-density map interpretation. Meth. Enzymol. 277B:1997;173-207.
20. Kool E.T. Active site tightness and substrate fit in DNA replication. Annu. Rev. Biochem. 71:2002;191-219.
21. Koradi R., Billeter M., Wüthrich K. Molmol. a program for display and analysis of macromolecular structures J. Mol. Graph. 14:1996;51-55.
22. Kraulis P. Molscript. A program to produce both detailed and schematic plots of protein structures J. Appl. Crystallogr. 24:1991;946-950.
23. Kunkel T.A., Bebenek K. DNA replication fidelity. Annu. Rev. Biochem. 69:2000;497-529.
24. Kurland C.G., Hughes D., Ehrenberg M. Limitations of translational accuracy. Neidhardt F.C., Curtiss R. III, Ingraham J.L., Lin E.C.C., Low K.B., Magasanik B. Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. 1996;American Society for Microbiology Press, Washington, DC. 979-1004.pp.
25. Lim V.I., Curran J.F. Analysis of codon. anticodon interactions within the ribosome provides new insights into codon reading and the genetic code structure RNA. 7:2001;942-957.
26. Lodmell J.S., Dahlberg A.E. A conformational switch in Escherichia coli 16S ribosomal RNA during decoding of messenger RNA. Science. 277:1997;1262-1267.
27. Mathews D.H., Sabina J., Zuker M., Turner D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288:1999;911-940.
28. Merritt E.A., Bacon D.J. Raster3D. photorealistic molecular graphics Meth. Enzymol. 277:1997;505-524.
29. Nierhaus K.H. The allosteric three-site model for the ribosomal elongation cycle. features and future Biochemistry. 29:1990;4997-5008.
30. Ninio J. Kinetic amplification of enzyme discrimination. Biochimie. 57:1975;587-595.
31. Nissen P., Ippolito J.A., Ban N., Moore P.B., Steitz T.A. RNA tertiary interactions in the large ribosomal subunit. the A-minor motif Proc. Natl. Acad. Sci. USA. 98:2001;4899-4903.
32. Ogle J.M., Brodersen D.E., Clemons W.M. Jr., Tarry M.J., Carter A.P., Ramakrishnan V. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science. 292:2001;897-902.
33. Otwinowski Z., Minor W. Processing of x-ray diffraction data collected in oscillation mode. Carter C.W.J., Sweet R.M. Methods Enzymol. 1997;Academic Press, New York. 307-325.pp.
34. Pape T., Wintermeyer W., Rodnina M. Induced fit in initial selection and proofreading of aminoacyl-tRNA on the ribosome. EMBO J. 18:1999;3800-3807.
35. Piepenburg O., Pape T., Pleiss J.A., Wintermeyer W., Uhlenbeck O.C., Rodnina M.V. Intact aminoacyl-tRNA is required to trigger GTP hydrolysis by elongation factor Tu on the ribosome. Biochemistry. 39:2000;1734-1738.
36. Pongs O., Bald R., Reinwald E. On the structure of yeast tRNAPhe. Complementary-oligonucleotide binding studies. Eur. J. Biochem. 32:1973;117-125.
37. Powers T., Noller H.F. Selective perturbation of G530 of 16 S rRNA by translational miscoding agents and a streptomycin-dependence mutation in protein S12. J. Mol. Biol. 235:1994;156-172.
38. Rodnina M.V., Wintermeyer W. Fidelity of aminoacyl-tRNA selection on the ribosome. kinetic and structural mechanisms Annu. Rev. Biochem. 70:2001;415-435.
39. Rodnina M.V., Fricke R., Wintermeyer W. Transient conformational states of aminoacyl-tRNA during ribosome binding catalyzed by elongation factor Tu. Biochemistry. 33:1994;12267-12275.
40. Schluenzen F., Tocilj A., Zarivach R., Harms J., Gluehmann M., Janell D., Bashan A., Bartels H., Agmon I., Franceschi F., Yonath A. Structure of functionally activated small ribosomal subunit at 3.3 Å resolution. Cell. 102:2000;615-623.
41. Schneider T.R. A genetic algorithm for the identification of conformationally invariant regions in protein molecules. Acta Crystallogr. D Biol. Crystallogr. 58:2002;195-208.
42. Seeman N.C., Rosenberg J.M., Rich A. Sequence-specific recognition of double helical nucleic acids by proteins. Proc. Natl. Acad. Sci. USA. 73:1976;804-808.
43. Thompson R.C., Stone P.J. Proofreading of the codon-anticodon interaction on ribosomes. Proc. Natl. Acad. Sci. USA. 74:1977;198-202.
44. Thompson R.C., Dix D.B. Accuracy of protein biosynthesis. A kinetic study of the reaction of poly(U)-programmed ribosomes with a leucyl-tRNA2-elongation factor Tu-GTP complex. J. Biol. Chem. 257:1982;6677-6682.
45. Uhlenbeck O.C., Martin F.H., Doty P. Self-complementary oligoribonucleotides. effects of helix defects and guanylic acid-cytidylic acid base pairs J. Mol. Biol. 57:1971;217-229.
46. Valle M., Sengupta J., Swami N.K., Grassucci R.A., Burkhardt N., Nierhaus K.H., Agrawal R.K., Frank J. Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process. EMBO J. 21:2002;3557-3567.
47. VanLoock M.S., Agrawal R.K., Gabashvili I.S., Qi L., Frank J., Harvey S.C. Movement of the decoding region of the 16 S ribosomal RNA accompanies tRNA translocation. J. Mol. Biol. 304:2000;507-515.
48. Wimberly B.T., Brodersen D.E., Clemons W.M., Morgan-Warren R.J., Carter A.P., Vonrhein C., Hartsch T., Ramakrishnan V. Structure of the 30S ribosomal subunit. Nature. 407:2000;327-339.
49. Xia T., SantaLucia J. Jr., Burkard M.E., Kierzek R., Schroeder S.J., Jiao X., Cox C., Turner D.H. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry. 37:1998;14719-14735.
50. Yarus M., Smith D. tRNA on the ribosome. a waggle theory Biosynthesis and Function D., Söll, RajBhandary U. tRNA. Structure:1995;American Society for Microbiology, Washington. 443-468.pp.
51. Yusupov M.M., Yusupova G.Z., Baucom A., Lieberman K., Earnest T.N., Cate J.H., Noller H.F. Crystal structure of the ribosome at 5.5 A resolution. Science. 292:2001;883-896.