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Structural basis for anticodon recognition by methionyl-tRNA synthetase

Nature Structural & Molecular Biology volume 12, pages 931–932 (2005)Cite this article

Abstract

In the 2.7-Å resolution crystal structure of methionyl-tRNA synthetase (MetRS) in complex with tRNAMet and a methionyl-adenylate analog, the tRNA anticodon loop is distorted to form a triple-base stack comprising C34, A35 and A38. A tryptophan residue stacks on C34 to extend the triple-base stack. In addition, C34 forms Watson-Crick–type hydrogen bonds with Arg357. This structure resolves the longstanding question of how MetRS specifically recognizes tRNAMet.

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Figure 1: The A. aeolicus MetRS–tRNAmMet complex.
Figure 2: Recognition of the anticodon CAU of tRNAmMet by MetRS.

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Acknowledgements

We thank M. Kawamoto and N. Shimizu (Japan Synchrotron Radiation Research Institute) for their help in data collection at SPring-8. This work was supported by a grant from the Ministry of Education, Culture, Sports, Science and Technology to O.N., by a Precursory Research for Embryonic Science and Technology Program grant from Japan Science and Technology and by Sumitomo and Naito Foundation grants to O.N.

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Authors and Affiliations

  1. Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa, 226-8501, Japan

    Kotaro Nakanishi, Yuri Ogiso, Takashi Nakama, Shuya Fukai & Osamu Nureki

  2. Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Honcho, Kawaguchi-shi, 332-0012, Saitama, Japan

    Takashi Nakama & Osamu Nureki

  3. Rikagaku Kenkyusho Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan

    Osamu Nureki

Authors
  1. Kotaro Nakanishi
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  2. Yuri Ogiso
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  3. Takashi Nakama
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  4. Shuya Fukai
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  5. Osamu Nureki
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Correspondence to Osamu Nureki.

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Supplementary information

Supplementary Fig. 1

MetSA bound to the amino-acylation site of MetRS (PDF 643 kb)

Supplementary Fig. 2

Conformational change of MetRS upon tRNAMetm binding (PDF 849 kb)

Supplementary Fig. 3

The 2|Fo|-|Fc| simulated annealing omit map (PDF 1173 kb)

Supplementary Fig. 4

Sequence alignment of MetRSs (PDF 1053 kb)

Supplementary Fig. 5

Comparison of tRNA anticodon recognition by the class Ia aaRSs (PDF 1853 kb)

Supplementary Table 1

Data collection and refinement statistics (PDF 63 kb)

Supplementary Methods (PDF 83 kb)

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Nakanishi, K., Ogiso, Y., Nakama, T. et al. Structural basis for anticodon recognition by methionyl-tRNA synthetase. Nat Struct Mol Biol 12, 931–932 (2005). https://doi.org/10.1038/nsmb988

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