A unique conformation of the anticodon stem-loop is associated with the capacity of tRNAfMet to initiate protein synthesis

Nucleic Acids Research

Volumn 36, Issue 15, 2008, Pages 4894-4901

  Barraud, Pierre ^a   Schmitt, Emmanuelle ^b   Mechulam, Yves ^b   Dardel, Frédéric ^a   Tisné, Carine ^a  

^a UNIVERSITÉ PARIS DESCARTES   (France)

^b LABORATOIRE DE BIOCHIMIE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSFER RNA METHYLTRANSFERASE;

ANISOTROPY; ANTICODON; ARTICLE; BASE PAIRING; CONTROLLED STUDY; CRYSTAL STRUCTURE; ESCHERICHIA COLI; GC RICH SEQUENCE; MOLECULAR MECHANICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; TRANSLATION INITIATION;

ANTICODON; BASE SEQUENCE; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PEPTIDE CHAIN INITIATION, TRANSLATIONAL; RNA, BACTERIAL; RNA, TRANSFER, MET;

ESCHERICHIA COLI;

EID: 50849106034     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn462     Document Type: Article

References (42)

1. Marck,C. and Grosjean,H. (2002) tRNomics: Analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. RNA, 8, 1189-1232.
2. Wrede,P., Woo,N.H. and Rich,A. (1979) Initiator tRNAs have a unique anticodon loop conformation. Proc. Natl Acad. Sci. USA, 76, 3289-3293.
3. Seong,B.L. and RajBhandary,U.L. (1987) Escherichia coli formylmethionine tRNA: Mutations in GGGCCC sequence conserved in anticodon stem of initiator tRNAs affect initiation of protein synthesis and conformation of anticodon loop. Proc. Natl Acad. Sci. USA, 84, 334-338.
4. Hartz,D., Binkley,J., Hollingsworth,T. and Gold,L. (1990) Domains of initiator tRNA and initiation codon crucial for initiator tRNA selection by Escherichia coli IF3. Genes Dev., 4, 1790-1800.
5. Varshney,U., Lee,C.P. and RajBhandary,U.L. (1993) From elongator tRNA to initiator tRNA. Proc. Natl Acad. Sci. USA, 90, 2305-2309.
6. Basavappa,R. and Sigler,P.B. (1991) The 3A crystal structure of yeast initiator tRNA: Functional implications in initiator/elongator discrimination. EMBO J., 10, 3105-3111.
7. Woo,N.H., Roe,B.A. and Rich,A. (1980) Three-dimensional structure of Escherichia coli initiator tRNAfMet. Nature, 286, 346-351.
8. Schweisguth,D.C. and Moore,P.B. (1997) On the conformation of the anticodon loops of initiator and elongator methionine tRNAs. J. Mol. Biol., 267, 505-519.
9. Selmer,M., Dunham,C.M., Murphy,F.V.t., Weixlbaumer,A., Petry,S., Kelley,A.C., Weir,J.R. and Ramakrishnan,V. (2006) Structure of the 70S ribosome complexed with mRNA and tRNA. Science, 313, 1935-1942.
10. Korostelev,A., Trakhanov,S., Laurberg,M. and Noller,H.F. (2006) Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell, 126, 1065-1077.
11. Yusupov,M.M., Yusupova,G.Z., Baucom,A., Lieberman,K., Earnest,T.N., Cate,J.H. and Noller,H.F. (2001) Crystal structure of the ribosome at 5.5A resolution. Science, 292, 883-896.
12. Korostelev,A. and Noller,H.F. (2007) The ribosome in focus: New structures bring new insights. Trends Biochem. Sci., 32, 434-441.
13. Nissen,P., Ippolito,J.A., Ban,N., Moore,P.B. and Steitz,T.A. (2001) RNA tertiary interactions in the large ribosomal subunit: The A-minor motif. Proc. Natl Acad. Sci. USA, 98, 4899-4903.
14. Abdi,N.M. and Fredrick,K. (2005) Contribution of 16S rRNA nucleotides forming the 30S subunit A and P sites to translation in Escherichia coli. RNA, 11, 1624-1632.
15. Lancaster,L. and Noller,H.F. (2005) Involvement of 16S rRNA nucleotides G1338 and A1339 in discrimination of initiator tRNA. Mol. Cell, 20, 623-632.
16. Mangroo,D., Limbach,P.A., McCloskey,J.A. and RajBhandary,U.L. (1995) An anticodon sequence mutant of Escherichia coli initiator tRNA: Possible importance of a newly acquired base modification next to the anticodon on its activity in initiation. J. Bacteriol., 177, 2858-2862.
17. Meinnel,T., Mechulam,Y. and Fayat,G. (1988) Fast purification of a functional elongator tRNAMet expressed from a synthetic gene in vivo. Nucleic Acids Res., 16, 8095-8096.
18. Collaborative Computational Project Number 4. (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D, 50 760-763.
19. Potterton,E., Briggs,P., Turkenburg,M. and Dodson,E. (2003) A graphical user interface to the CCP4 program suite. Acta Crystallogr. D, 59, 1131-1137.
20. Leslie,A.G. (2006) The integration of macromolecular diffraction data. Acta Crystallogr. D, 62, 48-57.
21. Evans,P. (2006) Scaling and assessment of data quality. Acta Crystallogr. D, 62, 72-82.
22. McCoy,A.J., Grosse-Kunstleve,R.W., Storoni,L.C. and Read,R.J. (2005) Likelihood-enhanced fast translation functions. Acta Crystallogr., 61, 458-464.
23. Emsley,P. and Cowtan,K. (2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr. D, 60, 2126-2132.
24. Winn,M.D., Isupov,M.N. and Murshudov,G.N. (2001) Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr. D, 57, 122-133.
25. Murshudov,G.N., Vagin,A.A. and Dodson,E.J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D, 53, 240-255.
26. Strong,M., Sawaya,M.R., Wang,S., Phillips,M., Cascio,D. and Eisenberg,D. (2006) Toward the structural genomics of complexes: Crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis. Proc. Natl Acad. Sci. USA, 103, 8060-8065.
27. Kim,S.H., Quigley,G.J., Suddath,F.L., McPherson,A., Sneden,D., Kim,J.J., Weinzierl,J. and Rich,A. (1973) Three-dimensional structure of yeast phenylalanine transfer RNA: Folding of the polynucleotide chain. Science, 179, 285-288.
28. Moras,D., Dock,A.C., Dumas,P., Westhof,E., Romby,P., Ebel,J.P. and Giege,R. (1986) Anticodon-anticodon interaction induces conformational changes in tRNA: Yeast tRNAAsp, a model for tRNA-mRNA recognition. Proc. Natl Acad. Sci. USA, 83, 932-936.
29. Auffinger,P. and Westhof,E. (1999) Singly and bifurcated hydrogenbonded base-pairs in tRNA anticodon hairpins and ribozymes. J. Mol. Biol. 292, 467-483.
30. Schmitt,E., Panvert,M., Blanquet,S. and Mechulam,Y. (1998) Crystal structure of methionyl-tRNAfMet transformylase complexed with the initiator formyl-methionyl-tRNAfMet. EMBO J., 17, 6819-6826.
31. Durant,P.C. and Davis,D.R. (1999) Stabilization of the anticodon stem-loop of tRNALys,3 by an A+-C base-pair and by pseudouridine. J. Mol. Biol., 285, 115-131.
32. Wakao,H., Romby,P., Westhof,E., Laalami,S., Grunberg-Manago, M., Ebel,J.P., Ehresmann,C. and Ehresmann,B. (1989) The solution structure of the Escherichia coli initiator tRNA and its interactions with initiation factor 2 and the ribosomal 30 S subunit. J. Biol. Chem. 264, 20363-20371.
33. Robertus,J.D., Ladner,J.E., Finch,J.T., Rhodes,D., Brown,R.S., Clark,B.F. and Klug,A. (1974) Structure of yeast phenylalanine tRNA at 3 Å resolution. Nature, 250, 546-551.
34. Suddath,F.L., Quigley,G.J., McPherson,A., Sneden,D., Kim,J.J., Kim,S.H. and Rich,A. (1974) Three-dimensional structure of yeast phenylalanine transfer RNA at 3.0angstroms resolution. Nature, 248, 20-24.
35. Jovine,L., Djordjevic,S. and Rhodes,D. (2000) The crystal structure of yeast phenylalanine tRNA at 2.0 A resolution: Cleavage by Mg(2+) in 15-year old crystals. J. Mol. Biol., 301, 401-414.
36. Shi,H. and Moore,P.B. (2000) The crystal structure of yeast phenylalanine tRNA at 1.93A resolution: A classic structure revisited. RNA, 6, 1091-1105.
37. Westhof,E., Dumas,P. and Moras,D. (1985) Crystallographic refinement of yeast aspartic acid transfer RNA. J. Mol. Biol., 184, 119-145.
38. Benas,P., Bee,G., Keith,G., Marquet,R., Ehresmann,C., Ehresmann,B. and Dumas,P. (2000) The crystal structure of HIV reverse-transcription primer tRNA(Lys,3) shows a canonical anticodon loop. RNA, 6, 1347-1355.
39. Ramesh,V., Mayer,C., Dyson,M.R., Gite,S. and RajBhandary,U.L. (1999) Induced fit of a peptide loop of methionyl-tRNA formyl-transferase triggered by the initiator tRNA substrate. Proc. Natl Acad. Sci. USA 96, 875-880.
40. Wrede,P. and Rich,A. (1979) Stability of the unique anticodon loop conformation of E.coli tRNAfMet. Nucleic Acids Res., 7, 1457-1467.
41. Berk,V., Zhang,W., Pai,R.D. and Cate,J.H. (2006) Structural basis for mRNA and tRNA positioning on the ribosome. Proc. Natl Acad. Sci. USA 103, 15830-15834.
42. Dallas,A. and Noller,H.F. (2001) Interaction of translation initiation factor 3 with the 30S ribosomal subunit. Mol. Cell, 8, 855-864.