Structure of substrate-bound SMG1-8-9 kinase complex reveals molecular basis for phosphorylation specificity

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

Abstract

PI3K-related kinases (PIKKs) are large Serine/Threonine (Ser/Thr)-protein kinases central to the regulation of many fundamental cellular processes. PIKK family member SMG1 orchestrates progression of an RNA quality control pathway, termed nonsense-mediated mRNA decay (NMD), by phosphorylating the NMD factor UPF1. Phosphorylation of UPF1 occurs in its unstructured N- and C-terminal regions at Serine/Threonine-Glutamine (SQ) motifs. How SMG1 and other PIKKs specifically recognize SQ motifs has remained unclear. Here, we present a cryo-electron microscopy (cryo-EM) reconstruction of a human SMG1-8-9 kinase complex bound to a UPF1 phosphorylation site at an overall resolution of 2.9 Å. This structure provides the first snapshot of a human PIKK with a substrate-bound active site. Together with biochemical assays, it rationalizes how SMG1 and perhaps other PIKKs specifically phosphorylate Ser/Thr-containing motifs with a glutamine residue at position +1 and a hydrophobic residue at position -1, thus elucidating the molecular basis for phosphorylation site recognition.

Data availability

EM data have been deposited in EMDB under the accession code EMD-11063. The model has been deposited in PDB under the accession 6Z3R.

The following data sets were generated

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. 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
  3. 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
  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 (PhD fellowship)

  • Lukas M Langer

Max-Planck-Gesellschaft

  • Elena Conti

European Commission (ERC Advanced Investigator Grant EXORICO)

  • Elena Conti

Deutsche Forschungsgemeinschaft (SFB1035,GRK1721,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

Publication history

  1. Received: March 21, 2020
  2. Accepted: May 28, 2020
  3. Accepted Manuscript published: May 29, 2020 (version 1)
  4. Version of Record published: July 3, 2020 (version 2)

Copyright

© 2020, 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. Yair Gat
  3. Fabien Bonneau
  4. Elena Conti
(2020)
Structure of substrate-bound SMG1-8-9 kinase complex reveals molecular basis for phosphorylation specificity
eLife 9:e57127.
https://doi.org/10.7554/eLife.57127

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