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Structural basis of enzyme encapsulation into a bacterial nanocompartment

Nature Structural & Molecular Biology volume 15, pages 939947 (2008) | Download Citation

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Abstract

Compartmentalization is an important organizational feature of life. It occurs at varying levels of complexity ranging from eukaryotic organelles and the bacterial microcompartments, to the molecular reaction chambers formed by enzyme assemblies. The structural basis of enzyme encapsulation in molecular compartments is poorly understood. Here we show, using X-ray crystallographic, biochemical and EM experiments, that a widespread family of conserved bacterial proteins, the linocin-like proteins, form large assemblies that function as a minimal compartment to package enzymes. We refer to this shell-forming protein as 'encapsulin'. The crystal structure of such a particle from Thermotoga maritima determined at 3.1-Å resolution reveals that 60 copies of the monomer assemble into a thin, icosahedral shell with a diameter of 240 Å. The interior of this nanocompartment is lined with conserved binding sites for short polypeptide tags present as C-terminal extensions of enzymes involved in oxidative-stress response.

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Acknowledgements

Crystallographic data were collected at the beamline X06SA at the Swiss Light Source (SLS). We are grateful to C. Schulze-Briese, E. Pohl and T. Tomizaki for their outstanding support at the SLS. We thank R. Brunisholz, P. Hunziker and Y. Auchli at the Functional Genomics Center Zurich for mass-spectrometric analysis, the Electron Microscopy Center Zurich (EMEZ) and Martin Beck for support with EM data collection, M. Müller, F. Voigts-Hoffmann and F. Imkamp for critically reading the manuscript and all members of the Ban and Weber-Ban laboratory for suggestions and discussions. D.B. was supported by a Federation of European Biochemical Societies long-term fellowship. This work was supported by the Swiss National Science Foundation (SNSF) (to N.B. and E.W.B.) and the National Center of Excellence in Research (NCCR) Structural Biology program of the SNSF (to N.B. and E.W.B.).

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Affiliations

  1. ETH Zurich, Institute of Molecular Biology and Biophysics, Schafmattstrasse 20, 8093 Zurich, Switzerland.

    • Markus Sutter
    • , Daniel Boehringer
    • , Eilika Weber-Ban
    •  & Nenad Ban
  2. Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4056 Basel, Switzerland.

    • Sascha Gutmann
  3. ETH Zurich, Institute of Food Science and Nutrition, Schmelzbergstrasse 9, 8092 Zurich, Switzerland.

    • Susanne Günther
    •  & Martin J Loessner
  4. Molecular Biology of the Gene in Extremophiles Unit, Institute Pasteur, rue Docteur Roux 25, 75724 Paris, Cedex 15, France.

    • David Prangishvili
  5. Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany.

    • Karl O Stetter

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Competing interests

The authors are planning on filing a pre-patent application on possible uses and applications of encapsulin in biotechnology and biomedicine.

Corresponding authors

Correspondence to Eilika Weber-Ban or Nenad Ban.

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https://doi.org/10.1038/nsmb.1473

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