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The structural basis of tRNA recognition by arginyl-tRNA-protein transferase

Author

Listed:
  • Thilini Abeywansha

    (Case Western Reserve University)

  • Wei Huang

    (Case Western Reserve University)

  • Xuan Ye

    (Case Western Reserve University
    Case Western Reserve University)

  • Allison Nawrocki

    (Case Western Reserve University)

  • Xin Lan

    (Case Western Reserve University)

  • Eckhard Jankowsky

    (Case Western Reserve University
    Case Western Reserve University
    Case Western Reserve University)

  • Derek J. Taylor

    (Case Western Reserve University
    Case Western Reserve University
    Case Western Reserve University)

  • Yi Zhang

    (Case Western Reserve University
    Case Western Reserve University)

Abstract

Arginyl-tRNA-protein transferase 1 (ATE1) is a master regulator of protein homeostasis, stress response, cytoskeleton maintenance, and cell migration. The diverse functions of ATE1 arise from its unique enzymatic activity to covalently attach an arginine onto its protein substrates in a tRNA-dependent manner. However, how ATE1 (and other aminoacyl-tRNA transferases) hijacks tRNA from the highly efficient ribosomal protein synthesis pathways and catalyzes the arginylation reaction remains a mystery. Here, we describe the three-dimensional structures of Saccharomyces cerevisiae ATE1 with and without its tRNA cofactor. Importantly, the putative substrate binding domain of ATE1 adopts a previously uncharacterized fold that contains an atypical zinc-binding site critical for ATE1 stability and function. The unique recognition of tRNAArg by ATE1 is coordinated through interactions with the major groove of the acceptor arm of tRNA. Binding of tRNA induces conformational changes in ATE1 that helps explain the mechanism of substrate arginylation.

Suggested Citation

  • Thilini Abeywansha & Wei Huang & Xuan Ye & Allison Nawrocki & Xin Lan & Eckhard Jankowsky & Derek J. Taylor & Yi Zhang, 2023. "The structural basis of tRNA recognition by arginyl-tRNA-protein transferase," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-38004-8
    DOI: 10.1038/s41467-023-38004-8
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    References listed on IDEAS

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    1. Kazunori Watanabe & Yukimatsu Toh & Kyoko Suto & Yoshihiro Shimizu & Natsuhisa Oka & Takeshi Wada & Kozo Tomita, 2007. "Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase," Nature, Nature, vol. 449(7164), pages 867-871, October.
    2. Kathryn Tunyasuvunakool & Jonas Adler & Zachary Wu & Tim Green & Michal Zielinski & Augustin Žídek & Alex Bridgland & Andrew Cowie & Clemens Meyer & Agata Laydon & Sameer Velankar & Gerard J. Kleywegt, 2021. "Highly accurate protein structure prediction for the human proteome," Nature, Nature, vol. 596(7873), pages 590-596, August.
    3. Yi Zhang & Su Ran Mun & Juan F. Linares & JaeWoo Ahn & Christina G. Towers & Chang Hoon Ji & Brent E. Fitzwalter & Michael R. Holden & Wenyi Mi & Xiaobing Shi & Jorge Moscat & Andrew Thorburn & Maria , 2018. "ZZ-dependent regulation of p62/SQSTM1 in autophagy," Nature Communications, Nature, vol. 9(1), pages 1-11, December.
    4. John Jumper & Richard Evans & Alexander Pritzel & Tim Green & Michael Figurnov & Olaf Ronneberger & Kathryn Tunyasuvunakool & Russ Bates & Augustin Žídek & Anna Potapenko & Alex Bridgland & Clemens Me, 2021. "Highly accurate protein structure prediction with AlphaFold," Nature, Nature, vol. 596(7873), pages 583-589, August.
    5. Verna Van & Janae B. Brown & Corin R. O’Shea & Hannah Rosenbach & Ijaz Mohamed & Nna-Emeka Ejimogu & Toan S. Bui & Veronika A. Szalai & Kelly N. Chacón & Ingrid Span & Fangliang Zhang & Aaron T. Smith, 2023. "Iron-sulfur clusters are involved in post-translational arginylation," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
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    Cited by:

    1. Aline Umuhire Juru & Rodolfo Ghirlando & Jinwei Zhang, 2024. "Structural basis of tRNA recognition by the widespread OB fold," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    2. Xin Lan & Wei Huang & Su Bin Kim & Dechen Fu & Thilini Abeywansha & Jiemin Lou & Udayakumaran Balamurugan & Yong Tae Kwon & Chang Hoon Ji & Derek J. Taylor & Yi Zhang, 2024. "Oligomerization and a distinct tRNA-binding loop are important regulators of human arginyl-transferase function," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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