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Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation

Nature Structural & Molecular Biology volume 16, pages 1109–1115 (2009)Cite this article

Abstract

tRNA precursors undergo a maturation process, involving nucleotide modifications and folding into the L-shaped tertiary structure. The N1-methylguanosine at position 37 (m1G37), 3′ adjacent to the anticodon, is essential for translational fidelity and efficiency. In archaea and eukaryotes, Trm5 introduces the m1G37 modification into all tRNAs bearing G37. Here we report the crystal structures of archaeal Trm5 (aTrm5) in complex with tRNALeu or tRNACys. The D2-D3 domains of aTrm5 discover and modify G37, independently of the tRNA sequences. D1 is connected to D2-D3 through a flexible linker and is designed to recognize the shape of the tRNA outer corner, as a hallmark of the completed L shape formation. This interaction by D1 lowers the Km value for tRNA, enabling the D2-D3 catalysis. Thus, we propose that aTrm5 provides the tertiary structure checkpoint in tRNA maturation.

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Figure 1: The overall structures of the aTrm5–tRNA–AdoMet complexes.
Figure 2: G37 recognition mechanisms by D2-D3.
Figure 3: The anticodon arm and D stem recognition mechanism by D2-D3.
Figure 4: The recognition of the tRNA outer corner by D1.
Figure 5: The importance of the interaction between D1 and the outer corner of the tRNA.
Figure 6: The effects of other tRNA modifications.

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Acknowledgements

We thank M. Kimoto and I. Hirao for their assistance with the melting temperature measurements. We also thank S. Sekine for his help in collecting diffraction data and the staff of the beamlines BL41XU at SPring-8 (Harima, Japan) and NW12A at the Photon Factory (Tsukuba, Japan) for their support during data collection. This work was supported by the Targeted Proteins Research Program (TPRP) from the Ministry of Education, Culture, Sports, Science, and Technology of Japan (MEXT), Grant-in-Aid for Scientific Research (KAKENHI) from the Japan Society for the Promotion of Science (JSPS) and MEXT, the 21st century COE program (Promotion of Basic Biosciences for the Understanding of Organisms' Uniqueness) and the Global COE Program (Integrative Life Science Based on the Study of Biosignaling Mechanisms) from MEXT. S.G.-I. was supported by the 21st century COE Program, the Global COE Program and the Research Fellowship for Young Scientists from JSPS, and M.K. was supported by the Research Fellowship for Young Scientists from JSPS.

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Authors and Affiliations

  1. Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan

    Sakurako Goto-Ito, Takuhiro Ito, Mitsuo Kuratani & Shigeyuki Yokoyama

  2. RIKEN Systems and Structural Biology Center, Kanagawa, Japan

    Sakurako Goto-Ito, Takuhiro Ito, Mitsuo Kuratani, Yoshitaka Bessho & Shigeyuki Yokoyama

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  1. Sakurako Goto-Ito
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  2. Takuhiro Ito
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Contributions

S.G.-I. performed the sample preparation of aTrm5 and tRNAs, the crystal structure determinations and the biochemical assays; T.I. provided advice and helped with the experiments; M.K. prepared aTrm56 and ArcTGT; all authors discussed the results. S.G.-I., T.I. and S.Y. wrote the manuscript; S.Y. supervised the work.

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Correspondence to Shigeyuki Yokoyama.

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Goto-Ito, S., Ito, T., Kuratani, M. et al. Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation. Nat Struct Mol Biol 16, 1109–1115 (2009). https://doi.org/10.1038/nsmb.1653

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