Cryo-EM reconstructions of inhibitor-bound SMG1 kinase reveal an autoinhibitory state dependent on SMG8

  1. Lukas M Langer
  2. Fabien Bonneau
  3. Yair Gat
  4. Elena Conti  Is a corresponding author
  1. Max Planck Institute of Biochemistry, Germany

Abstract

The PI3K-related kinase (PIKK) SMG1 monitors progression of metazoan nonsense-mediated mRNA decay (NMD) by phosphorylating the RNA helicase UPF1. Previous work has shown that the activity of SMG1 is impaired by small molecule inhibitors, is reduced by the SMG1 interactors SMG8 and SMG9, and is downregulated by the so-called SMG1 insertion domain. However, the molecular basis for this complex regulatory network has remained elusive. Here, we present cryo-electron microscopy reconstructions of human SMG1-9 and SMG1-8-9 complexes bound to either a SMG1 inhibitor or a non-hydrolyzable ATP analogue at overall resolutions ranging from 2.8 to 3.6 Å. These structures reveal the basis with which a small molecule inhibitor preferentially targets SMG1 over other PIKKs. By comparison with our previously reported substrate-bound structure (Langer et al. 2020), we show that the SMG1 insertion domain can exert an autoinhibitory function by directly blocking the substrate binding path as well as overall access to the SMG1 kinase active site. Together with biochemical analysis, our data indicate that SMG1 autoinhibition is stabilized by the presence of SMG8. Our results explain the specific inhibition of SMG1 by an ATP-competitive small molecule, provide insights into regulation of its kinase activity within the NMD pathway, and expand the understanding of PIKK regulatory mechanisms in general.

Data availability

Models have been deposited in the PDB under the accession codes 7PW4 (SMG1-8-9 bound to SMG1i), 7PW5 (SMG1-8-9 bound to SMG1i, with SMG8 C-terminus), 7PW6 (SMG1 body bound to SMG1i), 7PW7 (SMG1-9 bound to SMG1i), 7PW8 (SMG1-8-9 bound to AMPPNP) and 7PW9 (SMG1-9 bound to AMPPNP). The corresponding EM maps have been deposited in the EMDB under the accession codes EMD-13674, EMD-13675, EMD-13676, EMD-13677, EMD-13678 and EMD-13679.

Article and author information

Author details

  1. Lukas M Langer

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Munich, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9977-2427
  2. Fabien Bonneau

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Munich, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8787-7662
  3. Yair Gat

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Munich, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2338-9384
  4. Elena Conti

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Munich, Germany
    For correspondence
    conti@biochem.mpg.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1254-5588

Funding

Boehringer Ingelheim Fonds

  • Lukas M Langer

Max-Planck-Gesellschaft

  • Elena Conti

European Commission (ERC Advanced Investigator Grant EXORICO)

  • Elena Conti

Deutsche Forschungsgemeinschaft (SFB1035)

  • Elena Conti

Deutsche Forschungsgemeinschaft (GRK1721)

  • Elena Conti

Deutsche Forschungsgemeinschaft (SFB/TRR 237)

  • Elena Conti

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

Reviewing Editor

  1. Philip A Cole, Harvard Medical School, United States

Version history

  1. Preprint posted: July 28, 2021 (view preprint)
  2. Received: July 28, 2021
  3. Accepted: October 25, 2021
  4. Accepted Manuscript published: October 26, 2021 (version 1)
  5. Version of Record published: November 15, 2021 (version 2)

Copyright

© 2021, Langer 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. Lukas M Langer
  2. Fabien Bonneau
  3. Yair Gat
  4. Elena Conti
(2021)
Cryo-EM reconstructions of inhibitor-bound SMG1 kinase reveal an autoinhibitory state dependent on SMG8
eLife 10:e72353.
https://doi.org/10.7554/eLife.72353

Share this article

https://doi.org/10.7554/eLife.72353

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