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Structure of the active form of Dcp1–Dcp2 decapping enzyme bound to m7GDP and its Edc3 activator

Nature Structural & Molecular Biology volume 23, pages 982986 (2016) | Download Citation

Abstract

Elimination of the 5′ cap of eukaryotic mRNAs, known as decapping, is considered to be a crucial, irreversible and highly regulated step required for the rapid degradation of mRNA by Xrn1, the major cytoplasmic 5′-3′ exonuclease. Decapping is accomplished by the recruitment of a protein complex formed by the Dcp2 catalytic subunit and its Dcp1 cofactor. However, this complex has a low intrinsic enzymatic activity and requires several accessory proteins such as the Lsm1–7 complex, Pat1, Edc1–Edc2 and/or Edc3 to be fully active. Here we present the crystal structure of the active form of the yeast Kluyveromyces lactis Dcp1–Dcp2 enzyme bound to its product (m7GDP) and its potent activator Edc3. This structure of the Dcp1–Dcp2 complex bound to a cap analog further explains previously published data on substrate binding and provides hints as to the mechanism of Edc3-mediated Dcp2 activation.

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Acknowledgements

We are indebted to K. Breunig (Martin-Luther University Halle–Wittenberg, Germany) for the kind gift of the K. lactis yeast strain. We acknowledge SOLEIL and ESRF for provision of synchrotron radiation facilities. This work was supported by Ecole Polytechnique (M.G.), the Centre National pour la Recherche Scientifique (B.S. and M.G.) including specific support by the ATIP–AVENIR program (to M.G.), the Agence Nationale pour la Recherche (grant ANR-11-BSV8-009 to B.S. and M.G., study ANR-10-LABX-0030-INRT, performed under the program Investissements d'Avenir ANR-10-IDEX-0002-02 (to B.S.), the Ligue Contre le Cancer (Equipe Labellisée 2014) (to B.S.) and the CERBM–IGBMC and INSERM (to B.S.). C.C. is supported by a PhD fellowship from the French Ministère de l'Enseignement Supérieur et de la Recherche (MESR) and ENS Cachan.

Author information

Affiliations

  1. Laboratoire de Biochimie, Ecole Polytechnique, CNRS, Université Paris-Saclay, Palaiseau, France.

    • Clément Charenton
    • , Régis Back
    •  & Marc Graille
  2. Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.

    • Valerio Taverniti
    • , Claudine Gaudon-Plesse
    •  & Bertrand Séraphin
  3. Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.

    • Valerio Taverniti
    • , Claudine Gaudon-Plesse
    •  & Bertrand Séraphin
  4. Institut National de Santé et de Recherche Médicale (INSERM) U964, Illkirch, France.

    • Valerio Taverniti
    • , Claudine Gaudon-Plesse
    •  & Bertrand Séraphin
  5. Université de Strasbourg, Illkirch, France.

    • Valerio Taverniti
    • , Claudine Gaudon-Plesse
    •  & Bertrand Séraphin

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Contributions

C.C. performed the biochemical and crystallographic experiments. V.T. performed enzymatic assays. C.G.-P. and R.B. performed cloning, and C.G.-P. performed preliminary binding assays. C.C., B.S. and M.G. designed research. C.C., B.S. and M.G. analyzed the data and wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Bertrand Séraphin or Marc Graille.

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DOI

https://doi.org/10.1038/nsmb.3300

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