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Structural basis of tRNA agmatinylation essential for AUA codon decoding

Nature Structural & Molecular Biology volume 18, pages 1275–1280 (2011)Cite this article

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Abstract

The cytidine at the first position of the anticodon (C34) in the AUA codon-specific archaeal tRNAIle2 is modified to 2-agmatinylcytidine (agm2C or agmatidine), an agmatine-conjugated cytidine derivative, which is crucial for the precise decoding of the genetic code. Agm2C is synthesized by tRNAIle-agm2C synthetase (TiaS) in an ATP-dependent manner. Here we present the crystal structures of the Archaeoglobus fulgidus TiaS–tRNAIle2 complexed with ATP, or with AMPCPP and agmatine, revealing a previously unknown kinase module required for activating C34 by phosphorylation, and showing the molecular mechanism by which TiaS discriminates between tRNAIle2 and tRNAMet. In the TiaS–tRNAIle2–ATP complex, C34 is trapped within a pocket far away from the ATP-binding site. In the agmatine-containing crystals, C34 is located near the AMPCPP γ-phosphate in the kinase module, demonstrating that agmatine is essential for placing C34 in the active site. These observations also provide the structural dynamics for agm2C formation.

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Figure 1: Structure of the TiaS–tRNAIle2–ATP ternary complex.
Figure 2: tRNAIle2 recognition in the ternary complex.
Figure 3: Structural dynamics of the TiaS–tRNAIle2 complex.
Figure 4: Proposed model for agm2C formation.

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  • 23 October 2011

    In the version of this article initially published online, the last sentence of the abstract was misleading. The error has been corrected for the print, PDF and HTML versions of the article.

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Acknowledgements

We thank K. Tomita, K. Ito and S. Fukai for valuable and critical comments and suggestions for this manuscript. We thank the beamline staff at BL-17A of the Photon Factory for technical assistance during data collection. This work was supported by a Precursory Research for Embryonic Science and Technology (PRESTO) Program grant from the Japan Science and Technology Agency (JST) (to T.N.); by a Grant-in-Aid for Young Scientists from the Japan Society for the Promotion of Science (JSPS) (to T.N.); by a Grant-in-Aid for JSPS Fellows (to T.O. and S.K.); by grants from the Kurata Memorial Hitachi Science and Technology Foundation, the Nakajima Foundation, the Mochida Memorial Foundation for Medical and Pharmaceutical Research, the Sankyo Foundation of Life Science and the Noda Institute for Scientific Research (to T.N.); by Grants-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Culture, Sports, Science and Technology of Japan (to T.S.); and by a grant from the New Energy and Industrial Technology Development Organization (NEDO) (to T.S.).

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Authors and Affiliations

  1. Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan

    Takuo Osawa, Hideko Inanaga & Tomoyuki Numata

  2. Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan

    Satoshi Kimura, Naohiro Terasaka & Tsutomu Suzuki

  3. Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Saitama, Japan

    Tomoyuki Numata

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  1. Takuo Osawa
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Contributions

H.I. and T.N. prepared the tRNAIle2 for crystallography. H.I. constructed the protein expression system. T.O. carried out the protein purification, crystallization and structure determination. T.N. assisted with the structure determination. T.O. and H.I. prepared the TiaS mutants. S.K. and N.T. prepared the tRNA mutants. S.K. and N.T. conducted the biochemical analyses under the supervision of T.S., and T.O. and T.N. wrote the paper. All authors discussed the results and commented on the manuscript. T.N. supervised the work.

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Correspondence to Tomoyuki Numata.

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Supplementary Figures 1–8, Supplementary Tables 1 and 2, Supplementary Methods and Supplementary Discussion (PDF 5053 kb)

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Osawa, T., Kimura, S., Terasaka, N. et al. Structural basis of tRNA agmatinylation essential for AUA codon decoding. Nat Struct Mol Biol 18, 1275–1280 (2011). https://doi.org/10.1038/nsmb.2144

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