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Structural basis for sequence-independent substrate selection by eukaryotic wobble base tRNA deaminase ADAT2/3

Author

Listed:
  • Luciano G. Dolce

    (EMBL Grenoble)

  • Aubree A. Zimmer

    (The Ohio State University)

  • Laura Tengo

    (EMBL Grenoble)

  • Félix Weis

    (EMBL Heidelberg, Structural and Computational Biology Unit)

  • Mary Anne T. Rubio

    (The Ohio State University)

  • Juan D. Alfonzo

    (The Ohio State University)

  • Eva Kowalinski

    (EMBL Grenoble)

Abstract

The essential deamination of adenosine A34 to inosine at the wobble base is the individual tRNA modification with the greatest effects on mRNA decoding, empowering a single tRNA to translate three different codons. To date, many aspects of how eukaryotic deaminases specifically select their multiple substrates remain unclear. Here, using cryo-EM, we present the structure of a eukaryotic ADAT2/3 deaminase bound to a full-length tRNA, revealing that the enzyme distorts the anticodon loop, but in contrast to the bacterial enzymes, selects its substrate via sequence-independent contacts of eukaryote-acquired flexible or intrinsically unfolded motifs distal from the conserved catalytic core. A gating mechanism for substrate entry to the active site is identified. Our multi-step tRNA recognition model yields insights into how RNA editing by A34 deamination evolved, shaped the genetic code, and directly impacts the eukaryotic proteome.

Suggested Citation

  • Luciano G. Dolce & Aubree A. Zimmer & Laura Tengo & Félix Weis & Mary Anne T. Rubio & Juan D. Alfonzo & Eva Kowalinski, 2022. "Structural basis for sequence-independent substrate selection by eukaryotic wobble base tRNA deaminase ADAT2/3," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-34441-z
    DOI: 10.1038/s41467-022-34441-z
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    1. 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.
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    1. Chanjing Feng & Kaiyun Xin & Yanfei Du & Jingwen Zou & Xiaoxing Xing & Qi Xiu & Yijie Zhang & Rui Zhang & Weiwei Huang & Qinhu Wang & Cong Jiang & Xiaojie Wang & Zhensheng Kang & Jin-Rong Xu & Huiquan, 2024. "Unveiling the A-to-I mRNA editing machinery and its regulation and evolution in fungi," Nature Communications, Nature, vol. 15(1), pages 1-18, December.

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