Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

How mutations in tRNA distant from the anticodon affect the fidelity of decoding


The ribosome converts genetic information into protein by selecting aminoacyl tRNAs whose anticodons base-pair to an mRNA codon. Mutations in the tRNA body can perturb this process and affect fidelity. The Hirsh suppressor is a well-studied tRNATrp harboring a G24A mutation that allows readthrough of UGA stop codons. Here we present crystal structures of the 70S ribosome complexed with EF-Tu and aminoacyl tRNA (native tRNATrp, G24A tRNATrp or the miscoding A9C tRNATrp) bound to cognate UGG or near-cognate UGA codons, determined at 3.2-Å resolution. The A9C and G24A mutations lead to miscoding by facilitating the distortion of tRNA required for decoding. A9C accomplishes this by increasing tRNA flexibility, whereas G24A allows the formation of an additional hydrogen bond that stabilizes the distortion. Our results also suggest that each native tRNA will adopt a unique conformation when delivered to the ribosome that allows accurate decoding.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Overview of miscoding mutations and Trp-tRNATrp bound in the A/T state.
Figure 2: Comparison of cognate and near-cognate structures in the decoding center.
Figure 3: Miscoding by the G24A and A9C Trp-tRNATrp.

Accession codes

Primary accessions

Protein Data Bank


  1. 1

    Hirsh, D. Tryptophan tRNA of Escherichia coli. Nature 228, 57 (1970).

    CAS  Article  Google Scholar 

  2. 2

    Smith, D. & Yarus, M. Transfer RNA structure and coding specificity. II. A D-arm tertiary interaction that restricts coding range. J. Mol. Biol. 206, 503–511 (1989).

    CAS  Article  Google Scholar 

  3. 3

    Smith, D. & Yarus, M. Transfer RNA structure and coding specificity. I. Evidence that a D-arm mutation reduces tRNA dissociation from the ribosome. J. Mol. Biol. 206, 489–501 (1989).

    CAS  Article  Google Scholar 

  4. 4

    Schultz, D.W. & Yarus, M. tRNA structure and ribosomal function. I. tRNA nucleotide 27–43 mutations enhance first position wobble. J. Mol. Biol. 235, 1381–1394 (1994).

    CAS  Article  Google Scholar 

  5. 5

    Ortiz-Meoz, R.F. & Green, R. Functional elucidation of a key contact between tRNA and the large ribosomal subunit rRNA during decoding. RNA 16, 2002–2013 (2010).

    CAS  Article  Google Scholar 

  6. 6

    Favre, A., Buchingham, R. & Thomas, G. tRNA tertiary structure in solution as probed by the photochemically induced 8–13 cross-link. Nucleic Acids Res. 2, 1421–1431 (1975).

    CAS  Article  Google Scholar 

  7. 7

    Cochella, L. & Green, R. An active role for tRNA in decoding beyond codon:anticodon pairing. Science 308, 1178–1180 (2005).

    CAS  Article  Google Scholar 

  8. 8

    Ogle, J.M. et al. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292, 897–902 (2001).

    CAS  Article  Google Scholar 

  9. 9

    Agris, P.F., Vendeix, F.A. & Graham, W.D. tRNA's wobble decoding of the genome: 40 years of modification. J. Mol. Biol. 366, 1–13 (2007).

    CAS  Article  Google Scholar 

  10. 10

    Pape, T., Wintermeyer, W. & Rodnina, M. Induced fit in initial selection and proofreading of aminoacyl-tRNA on the ribosome. EMBO J. 18, 3800–3807 (1999).

    CAS  Article  Google Scholar 

  11. 11

    Parker, J. Errors and alternatives in reading the universal genetic code. Microbiol. Rev. 53, 273–298 (1989).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. 12

    Fersht, A.R. The hydrogen bond in molecular recognition. Trends Biochem. Sci. 12, 301–304 (1987).

    CAS  Article  Google Scholar 

  13. 13

    Voorhees, R.M., Schmeing, T.M., Kelley, A.C. & Ramakrishnan, V. The mechanism for activation of GTP hydrolysis on the ribosome. Science 330, 835–838 (2010).

    CAS  Article  Google Scholar 

  14. 14

    Schmeing, T.M. et al. The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA. Science 326, 688–694 (2009).

    CAS  Article  Google Scholar 

  15. 15

    Murphy, F.V., Ramakrishnan, V., Malkiewicz, A. & Agris, P.F. The role of modifications in codon discrimination by tRNALysUUU . Nat. Struct. Mol. Biol. 11, 1186–1191 (2004).

    CAS  Article  Google Scholar 

  16. 16

    Olejniczak, M. & Uhlenbeck, O.C. tRNA residues that have coevolved with their anticodon to ensure uniform and accurate codon recognition. Biochimie 88, 943–950 (2006).

    CAS  Article  Google Scholar 

  17. 17

    Lowe, T.M. & Eddy, S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964 (1997).

    CAS  Article  Google Scholar 

  18. 18

    Shi, H. & Moore, P.B. The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: a classic structure revisited. RNA 6, 1091–1105 (2000).

    CAS  Article  Google Scholar 

  19. 19

    Nissen, P. et al. Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. Science 270, 1464–1472 (1995).

    CAS  Article  Google Scholar 

  20. 20

    Li, W. et al. Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM. EMBO J. 27, 3322–3331 (2008).

    CAS  Article  Google Scholar 

  21. 21

    Leontis, N.B. & Westhof, E. Geometric nomenclature and classification of RNA base pairs. RNA 7, 499–512 (2001).

    CAS  Article  Google Scholar 

  22. 22

    Fahlman, R.P., Dale, T. & Uhlenbeck, O.C. Uniform binding of aminoacylated transfer RNAs to the ribosomal A and P sites. Mol. Cell 16, 799–805 (2004).

    CAS  Article  Google Scholar 

  23. 23

    Gao, Y.G. et al. The structure of the ribosome with elongation factor G trapped in the posttranslocational state. Science 326, 694–699 (2009).

    CAS  Article  Google Scholar 

  24. 24

    Selmer, M. et al. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313, 1935–1942 (2006).

    CAS  Article  Google Scholar 

  25. 25

    Eisenberg, S.P., Söll, L. & Yarus, M. The purification and sequence of a temperature-sensitive tryptophan tRNA. J. Biol. Chem. 254, 5562–5566 (1979).

    CAS  PubMed  Google Scholar 

  26. 26

    McCarthy, A.A. et al. A decade of user operation on the macromolecular crystallography MAD beamline ID14–4 at the ESRF. J. Synchrotron Radiat. 16, 803–812 (2009).

    Article  Google Scholar 

  27. 27

    Kabsch, W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 26, 795–800 (1993).

    CAS  Article  Google Scholar 

  28. 28

    Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).

    Article  Google Scholar 

  29. 29

    Brünger, A.T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54, 905–921 (1998).

    Article  Google Scholar 

Download references


We thank R. Green and R. Ortiz-Meoz, Johns Hopkins University, for plasmids and bacterial strains for production of mutant tRNATrp, A. McCarthy and S. Brockhauser at ESRF ID14.4 for facilitating data collection, O. Uhlenbeck for helpful discussion and F. Murphy for scripting. This work was supported by the Medical Research Council, the Wellcome Trust, the Agouron Institute and the Louis-Jeantet Foundation. R.M.V. received support from the Gates-Cambridge scholarship. T.M.S. received support from the Human Frontier Science Program and Emmanuel College.

Author information




T.M.S. and R.M.V. designed the experiments, prepared and crystallized the ribosomal complexes, collected and processed X-ray crystallography data, determined, refined and analyzed the structures, and prepared the manuscript and figures. A.C.K. purified macromolecular components, prepared and crystallized ribosomal complexes and aided with collection of X-ray crystallography data. V.R. suggested the study and provided intellectual input and supervision.

Corresponding author

Correspondence to T Martin Schmeing.

Ethics declarations

Competing interests

V.R. is on the Senior Advisory Board of Rib-X Pharmaceuticals and both T.M.S. and V.R. hold stock options.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–3 (PDF 1078 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Schmeing, T., Voorhees, R., Kelley, A. et al. How mutations in tRNA distant from the anticodon affect the fidelity of decoding. Nat Struct Mol Biol 18, 432–436 (2011).

Download citation

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing