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The crystal structure of leucyl-tRNA synthetase complexed with tRNALeu in the post-transfer–editing conformation

Nature Structural & Molecular Biology volume 12, pages 923–930 (2005)Cite this article

Abstract

Leucyl-tRNA synthetase (LeuRS) has a specific post-transfer editing activity directed against mischarged isoleucine and similar noncognate amino acids. We describe the post-transfer–editing and product complexes of Thermus thermophilus LeuRS (LeuRSTT) with tRNALeu at 2.9- to 3.3-Å resolution. In the post-transfer–editing configuration, A76 binds in the editing active site exactly as previously found for the adenosine moiety of a small-molecule editing-substrate analog. The 60 C-terminal residues of LeuRSTT, unseen in previous structures, fold into a compact domain flexibly linked to the rest of the molecule and interacting with the G19-C56 tertiary base pair of tRNALeu. LeuRS recognition of tRNALeu depends essentially on tRNA shape rather than base-specific interactions. The structures show that considerable domain rotations, notably of the editing domain, accompany the tRNA–3′ end dynamics associated successively with aminoacylation, post-transfer editing and product release.

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Figure 1: Overall structure of the complex.
Figure 2: Structural comparison of the long-variable-arm tRNAs.
Figure 3: Structure and interactions of tRNALeu.
Figure 4: tRNA interactions with the editing domain.
Figure 5: Translocation from the aminoacylation to the editing configuration.

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Acknowledgements

The authors thank the European Synchrotron Radiation Facility (ESRF)–European Molecular Biology Laboratory Joint Structural Biology Group for access to ESRF synchrotron beamline facilities. A.Y. was supported in part by the Human Frontiers Science Programme Research grant RGP0190/2001-M and M.T. by US National Institutes of Health grant GM63107 to S. Martinis.

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Author notes

  1. Michael Tukalo and Anna Yaremchuk: These authors contributed equally to this work.

Authors and Affiliations

  1. European Molecular Biology Laboratory, Grenoble Outstation, c/o Institut Laue-Langevin, 156X, Grenoble, F-38042 Cedex 9, France

    Michael Tukalo, Anna Yaremchuk & Stephen Cusack

  2. Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev, 252627 143, Ukraine

    Michael Tukalo & Anna Yaremchuk

  3. Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan

    Ryuya Fukunaga & Shigeyuki Yokoyama

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  1. Michael Tukalo
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  5. Stephen Cusack
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Correspondence to Stephen Cusack.

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Supplementary information

Supplementary Fig. 1

Multiple sequence alignment of the C-terminal domain of representative bacteria and organellar LeuRS showing conservation of key residues. (PDF 68 kb)

Supplementary Fig. 2

Simulated omit map Fo-Fc electron density for the 3′ end of tRNALeu and Nva2AA. (PDF 302 kb)

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Tukalo, M., Yaremchuk, A., Fukunaga, R. et al. The crystal structure of leucyl-tRNA synthetase complexed with tRNALeu in the post-transfer–editing conformation. Nat Struct Mol Biol 12, 923–930 (2005). https://doi.org/10.1038/nsmb986

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