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The multicatalytic compartment of propionyl-CoA synthase sequesters a toxic metabolite

Nature Chemical Biology volume 14, pages 1127–1132 (2018)Cite this article

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Abstract

Cells must cope with toxic or reactive intermediates formed during metabolism. One coping strategy is to sequester reactions that produce such intermediates within specialized compartments or tunnels connecting different active sites. Here, we show that propionyl-CoA synthase (PCS), an ∼ 400-kDa homodimer, three-domain fusion protein and the key enzyme of the 3-hydroxypropionate bi-cycle for CO2 fixation, sequesters its reactive intermediate acrylyl-CoA. Structural analysis showed that PCS forms a multicatalytic reaction chamber. Kinetic analysis suggested that access to the reaction chamber and catalysis are synchronized by interdomain communication. The reaction chamber of PCS features three active sites and has a volume of only 33 nm3. As one of the smallest multireaction chambers described in biology, PCS may inspire the engineering of a new class of dynamically regulated nanoreactors.

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Fig. 1: Trifunctional PCS: structure and reaction sequence.
Fig. 2: PCS sequesters the reactive intermediate acrylyl-CoA.
Fig. 3: Multicatalytic reaction chamber of PCS.
Fig. 4: Proposed catalytic cycle of PCS.

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Data availability

The coordinates and structure factors of the crystal structure generated from this research are available in the Protein Data Bank under accession number PDB 6EQO. All other relevant data are available in this article and its supplementary information files, or from the corresponding author upon reasonable request.

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Acknowledgements

We thank T. Glatter for conceptualizing the limited proteolysis experiments and P. Pausch for help in collecting SAXS data. We acknowledge support from the European Synchrotron Radiation (ESRF, beamlines ID29, BM30 and BM29), Grenoble, France, and the Synchrotron SOLEIL (beamline PX-2A), Paris, France. The work conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under contract no. DE-AC02-05CH11231, granted to T.J.E. This work was funded by the Deutsche Forschungsgemeinschaft through Collaborative Research Centre SFB 987, the European Research Council (ERC 637675 ‘SYBORG’), a FET-Open Grant 686330 (‘FutureAgriculture’), the Gebert-Rüf-Stiftung (GRS 062-12) and the Max-Planck-Society, all granted to T.J.E.

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Author notes

  1. These authors contributed equally: Iria Bernhardsgrütter, Bastian Vögeli.

Authors and Affiliations

  1. Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany

    Iria Bernhardsgrütter, Bastian Vögeli, Dominik M. Peter, Niña Socorro Cortina, Jan Zarzycki & Tobias J. Erb

  2. Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany

    Tristan Wagner & Seigo Shima

  3. Proteomics Core Facility, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany

    Jörg Kahnt

  4. LOEWE Center for Synthetic Microbiology (Synmikro), Marburg, Germany

    Gert Bange

  5. Faculty of Chemistry, Philipps-University-Marburg, Marburg, Germany

    Gert Bange

  6. Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France

    Sylvain Engilberge & Eric Girard

  7. Laboratoire de Chimie, École Normale Supérieure de Lyon, Lyon, France

    François Riobé & Olivier Maury

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Contributions

I.B., B.V., D.M.P., J.Z. and T.J.E. conceived the project. I.B., B.V., T.W., J.Z. and T.J.E. designed and performed experiments and analyzed the data. E.G., F.R. and O.M. designed and prepared the phasing compound Tb-Xo4. I.B., B.V., S.E., E.G., T.W. and J.Z. collected X-ray datasets, and T.W. and J.Z. solved crystal structures. E.G., G.B., and S.S oversaw crystallography and SAXS experiments and provided equipment and beam time. J.K. performed peptide-labeling experiments. N.S.C. and J.K. performed mass spectrometry and analyzed the data. I.B., B.V., T.W., J.Z. and T.J.E. wrote the manuscript with contributions from all other authors.

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Correspondence to Tobias J. Erb.

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Bernhardsgrütter, I., Vögeli, B., Wagner, T. et al. The multicatalytic compartment of propionyl-CoA synthase sequesters a toxic metabolite. Nat Chem Biol 14, 1127–1132 (2018). https://doi.org/10.1038/s41589-018-0153-x

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