IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-50730-1.html
   My bibliography  Save this article

Structural basis of tRNA recognition by the widespread OB fold

Author

Listed:
  • Aline Umuhire Juru

    (National Institute of Diabetes and Digestive and Kidney Diseases)

  • Rodolfo Ghirlando

    (National Institute of Diabetes and Digestive and Kidney Diseases)

  • Jinwei Zhang

    (National Institute of Diabetes and Digestive and Kidney Diseases)

Abstract

The widespread oligonucleotide/oligosaccharide-binding (OB)-fold recognizes diverse substrates from sugars to nucleic acids and proteins, and plays key roles in genome maintenance, transcription, translation, and tRNA metabolism. OB-containing bacterial Trbp and yeast Arc1p proteins are thought to recognize the tRNA elbow or anticodon regions. Here we report a 2.6 Å co-crystal structure of Aquifex aeolicus Trbp111 bound to tRNAIle, which reveals that Trbp recognizes tRNAs solely by capturing their 3′ ends. Structural, mutational, and biophysical analyses show that the Trbp/EMAPII-like OB fold precisely recognizes the single-stranded structure, 3′ terminal location, and specific sequence of the 3′ CA dinucleotide — a universal feature of mature tRNAs. Arc1p supplements its OB – tRNA 3′ end interaction with additional contacts that involve an adjacent basic region and the tRNA body. This study uncovers a previously unrecognized mode of tRNA recognition by an ancient protein fold, and provides insights into protein-mediated tRNA aminoacylation, folding, localization, trafficking, and piracy.

Suggested Citation

  • 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.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-50730-1
    DOI: 10.1038/s41467-024-50730-1
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-50730-1
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-024-50730-1?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Jonah Beenstock & Samara Mishelle Ona & Jennifer Porat & Stephen Orlicky & Leo C. K. Wan & Derek F. Ceccarelli & Pierre Maisonneuve & Rachel K. Szilard & Zhe Yin & Dheva Setiaputra & Daniel Y. L. Mao , 2020. "A substrate binding model for the KEOPS tRNA modifying complex," Nature Communications, Nature, vol. 11(1), pages 1-17, December.
    2. Iris V. Hood & Jackson M. Gordon & Charles Bou-Nader & Frances E. Henderson & Soheila Bahmanjah & Jinwei Zhang, 2019. "Crystal structure of an adenovirus virus-associated RNA," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    3. 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.
    4. Atlanta G. Cook & Noemi Fukuhara & Martin Jinek & Elena Conti, 2009. "Structures of the tRNA export factor in the nuclear and cytosolic states," Nature, Nature, vol. 461(7260), pages 60-65, September.
    5. Alexey Bochkarev & Richard A. Pfuetzner & Aled M. Edwards & Lori Frappier, 1997. "Structure of the single-stranded-DNA-binding domain of replication protein A bound to DNA," Nature, Nature, vol. 385(6612), pages 176-181, January.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Krishna C. Suddala & Janghyun Yoo & Lixin Fan & Xiaobing Zuo & Yun-Xing Wang & Hoi Sung Chung & Jinwei Zhang, 2023. "Direct observation of tRNA-chaperoned folding of a dynamic mRNA ensemble," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    2. Marie-Claire Daugeron & Sophia Missoury & Violette Cunha & Noureddine Lazar & Bruno Collinet & Herman Tilbeurgh & Tamara Basta, 2023. "A paralog of Pcc1 is the fifth core subunit of the KEOPS tRNA-modifying complex in Archaea," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    3. 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.
    4. Charles Bou-Nader & Ankur Bothra & David N. Garboczi & Stephen H. Leppla & Jinwei Zhang, 2022. "Structural basis of R-loop recognition by the S9.6 monoclonal antibody," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    5. Sahiti Kuppa & Jaigeeth Deveryshetty & Rahul Chadda & Jenna R. Mattice & Nilisha Pokhrel & Vikas Kaushik & Angela Patterson & Nalini Dhingra & Sushil Pangeni & Marisa K. Sadauskas & Sajad Shiekh & Ham, 2022. "Rtt105 regulates RPA function by configurationally stapling the flexible domains," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    6. Aditi Mukherjee & Zakir Hossain & Esteban Erben & Shuai Ma & Jun Yong Choi & Hee-Sook Kim, 2023. "Identification of a small-molecule inhibitor that selectively blocks DNA-binding by Trypanosoma brucei replication protein A1," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    7. Seong-Su Han & Kuo-Kuang Wen & María L. García-Rubio & Marc S. Wold & Andrés Aguilera & Wojciech Niedzwiedz & Yatin M. Vyas, 2022. "WASp modulates RPA function on single-stranded DNA in response to replication stress and DNA damage," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    8. Poonam Roshan & Sahiti Kuppa & Jenna R. Mattice & Vikas Kaushik & Rahul Chadda & Nilisha Pokhrel & Brunda R. Tumala & Aparna Biswas & Brian Bothner & Edwin Antony & Sofia Origanti, 2023. "An Aurora B-RPA signaling axis secures chromosome segregation fidelity," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    9. Jina Yu & Chunli Yan & Tanmoy Paul & Lucas Brewer & Susan E. Tsutakawa & Chi-Lin Tsai & Samir M. Hamdan & John A. Tainer & Ivaylo Ivanov, 2024. "Molecular architecture and functional dynamics of the pre-incision complex in nucleotide excision repair," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-50730-1. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.