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The role of modifications in codon discrimination by tRNALysUUU

Nature Structural & Molecular Biology volume 11, pages 1186–1191 (2004)Cite this article

Abstract

The natural modification of specific nucleosides in many tRNAs is essential during decoding of mRNA by the ribosome. For example, tRNALysUUU requires the modification N6-threonylcarbamoyladenosine at position 37 (t6A37), adjacent and 3′ to the anticodon, to bind AAA in the A site of the ribosomal 30S subunit. Moreover, it can only bind both AAA and AAG lysine codons when doubly modified with t6A37 and either 5-methylaminomethyluridine or 2-thiouridine at the wobble position (mnm5U34 or s2U34). Here we report crystal structures of modified tRNA anticodon stem-loops bound to the 30S ribosomal subunit with lysine codons in the A site. These structures allow the rationalization of how modifications in the anticodon loop enable decoding of both lysine codons AAA and AAG.

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Figure 1: ASL sequence and modified nucleoside structures.
Figure 2: 2Fo − Fc density for the t6A37.
Figure 3: Stacking interactions of t6A37.
Figure 4: mnm5U·G, U-A and U·G base pairs.

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Acknowledgements

The authors acknowledge the contributions of W. Czestkowski for his modified nucleoside synthetic work, W. Graham for his purification of the doubly modified ASL, M. DeRider for contributions to structural modeling and J. Ogle for comments on the manuscript. This work was funded by the Medical Research Council, UK, US National Institutes of Health (NIH) grant GM67624 and a grant from the Agouron Institute (V.R.); US National Science Foundation grant MCB9986011 and NIH grant GM23037 (P.F.A.); and by the grant KBN 7TO9A01721 (A.M.). F.V.M. was supported by a European Molecular Biology Organization long term fellowship.

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Authors and Affiliations

  1. Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK

    Frank V Murphy IV & Venki Ramakrishnan

  2. Institute of Organic Chemistry, Technical University, Lodz, Poland

    Andrzej Malkiewicz

  3. Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, 27695-7622, North Carolina, USA

    Paul F Agris

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  1. Frank V Murphy IV
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Correspondence to Venki Ramakrishnan or Paul F Agris.

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Murphy, F., Ramakrishnan, V., Malkiewicz, A. et al. The role of modifications in codon discrimination by tRNALysUUU. Nat Struct Mol Biol 11, 1186–1191 (2004). https://doi.org/10.1038/nsmb861

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