Abstract

RtcB enzymes are RNA ligases that play essential roles in tRNA splicing, unfolded protein response, and RNA repair. In metazoa, RtcB functions as part of a five-subunit tRNA ligase complex (tRNA-LC) along with Ddx1, Cgi-99, Fam98B and Ashwin. The human tRNA-LC or its individual subunits have been implicated in additional cellular processes including microRNA maturation, viral replication, DNA double-strand break repair and mRNA transport. Here we present a biochemical analysis of the inter-subunit interactions within the human tRNA-LC along with crystal structures of the catalytic subunit RTCB and the N-terminal domain of CGI-99. We show that the core of the human tRNA-LC is assembled from RTCB and the C-terminal alpha-helical regions of DDX1, CGI-99, and FAM98B, all of which are required for complex integrity. The N-terminal domain of CGI-99 displays structural homology to calponin-homology domains, and CGI-99 and FAM98B associate via their N-terminal domains to form a stable subcomplex. The crystal structure of GMP-bound RTCB reveals divalent metal coordination geometry in the active site, providing insights into its catalytic mechanism. Collectively, these findings shed light on the molecular architecture and mechanism of the human tRNA ligase complex, and provide a structural framework for understanding its functions in cellular RNA metabolism.

Data availability

X-ray diffraction data and atomic models have been deposited in the Protein Data Bank under accession codes 7P3A (CGI-99 N-terminal domain) and 7P3B (RTCB in complex with GMP and Co(II)).The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD025662

The following data sets were generated

Article and author information

Author details

  1. Alena Kroupova

    Department of Biochemistry, University of Zurich, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  2. Fabian Ackle

    Department of Biochemistry, University of Zurich, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7199-5004
  3. Igor Asanović

    Max Perutz Laboratories, Medical University of Vienna, Vienna, Austria
    Competing interests
    The authors declare that no competing interests exist.
  4. Stefan Weitzer

    Max Perutz Laboratories, Medical University of Vienna, Vienna, Austria
    Competing interests
    The authors declare that no competing interests exist.
  5. Franziska M Boneberg

    Department of Biochemistry, University of Zurich, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  6. Marco Faini

    Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  7. Alexander Leitner

    Department of Biology, University of Konstanz, Konstanz, Germany
    Competing interests
    The authors declare that no competing interests exist.
  8. Alessia Chui

    Department of Biochemistry, University of Zurich, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  9. Ruedi Aebersold

    Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  10. Javier Martinez

    Max Perutz Laboratories, Medical University of Vienna, Vienna, Austria
    Competing interests
    The authors declare that no competing interests exist.
  11. Martin Jinek

    Department of Biochemistry, University of Zurich, Zurich, Switzerland
    For correspondence
    jinek@bioc.uzh.ch
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7601-210X

Funding

Boehringer Ingelheim Fonds (PhD Fellowship)

  • Alena Kroupova

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (NCCR RNA & Disease)

  • Alena Kroupova
  • Fabian Ackle
  • Franziska M Boneberg
  • Alexander Leitner
  • Martin Jinek

Fonds zur Forderung der wissenschaftlichen Forschung (P29888)

  • Igor Asanović
  • Stefan Weitzer
  • Javier Martinez

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Timothy W Nilsen, Case Western Reserve University, United States

Version history

  1. Received: June 25, 2021
  2. Preprint posted: July 12, 2021 (view preprint)
  3. Accepted: December 1, 2021
  4. Accepted Manuscript published: December 2, 2021 (version 1)
  5. Version of Record published: December 13, 2021 (version 2)

Copyright

© 2021, Kroupova et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Alena Kroupova
  2. Fabian Ackle
  3. Igor Asanović
  4. Stefan Weitzer
  5. Franziska M Boneberg
  6. Marco Faini
  7. Alexander Leitner
  8. Alessia Chui
  9. Ruedi Aebersold
  10. Javier Martinez
  11. Martin Jinek
(2021)
Molecular architecture of the human tRNA ligase complex
eLife 10:e71656.
https://doi.org/10.7554/eLife.71656

Share this article

https://doi.org/10.7554/eLife.71656

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