Letter | Published:

A four-helix bundle stores copper for methane oxidation

Nature volume 525, pages 140143 (03 September 2015) | Download Citation

Abstract

Methane-oxidizing bacteria (methanotrophs) require large quantities of copper for the membrane-bound (particulate) methane monooxygenase1,2. Certain methanotrophs are also able to switch to using the iron-containing soluble methane monooxygenase to catalyse methane oxidation, with this switchover regulated by copper3,4. Methane monooxygenases are nature’s primary biological mechanism for suppressing atmospheric levels of methane, a potent greenhouse gas. Furthermore, methanotrophs and methane monooxygenases have enormous potential in bioremediation and for biotransformations producing bulk and fine chemicals, and in bioenergy, particularly considering increased methane availability from renewable sources and hydraulic fracturing of shale rock5,6. Here we discover and characterize a novel copper storage protein (Csp1) from the methanotroph Methylosinus trichosporium OB3b that is exported from the cytosol, and stores copper for particulate methane monooxygenase. Csp1 is a tetramer of four-helix bundles with each monomer binding up to 13 Cu(I) ions in a previously unseen manner via mainly Cys residues that point into the core of the bundle. Csp1 is the first example of a protein that stores a metal within an established protein-folding motif. This work provides a detailed insight into how methanotrophs accumulate copper for the oxidation of methane. Understanding this process is essential if the wide-ranging biotechnological applications of methanotrophs are to be realized. Cytosolic homologues of Csp1 are present in diverse bacteria, thus challenging the dogma that such organisms do not use copper in this location.

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Accessions

Primary accessions

Data deposits

Atomic coordinates have been deposited in the Protein Data Bank under accession numbers 5AJE and 5AJF for apo- and Cu(I)-Csp1 respectively.

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Acknowledgements

We thank staff of the Diamond Light Source for help with diffraction data collection, J. Gray for performing mass spectrometry studies, the School of Civil Engineering and Geosciences and D. Graham for access to facilities at the very start of this work, A. Badarau for discussions about determining Cu(I) affinities and S. J. Firbank for structural modelling at the initial stages of this project. This work was supported by Biotechnology and Biological Sciences Research Council (grant BB/K008439/1 to C.D. and K.J.W.) and Newcastle University (part funding of a PhD studentship for S.P.). K.J.W. was supported by a Sir Henry Dale Fellowship funded by the Wellcome Trust and the Royal Society (098375/Z/12/Z).

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Author notes

    • Stephen J. Allen

    Present address: Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, Illinois 60208-2850, USA.

Affiliations

  1. Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK

    • Nicolas Vita
    • , Semeli Platsaki
    • , Arnaud Baslé
    • , Stephen J. Allen
    • , Kevin J. Waldron
    •  & Christopher Dennison
  2. Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK

    • Neil G. Paterson
  3. School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK

    • Andrew T. Crombie
    •  & J. Colin Murrell

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Contributions

C.D. and K.J.W. designed the research, N.V. and S.J.A. performed in vitro characterization of Csp1 and Cu(I) binding, S.P. isolated Csp1 from M. trichosporium OB3b and crystallized the protein, A.B. and N.G.P. solved the crystal structures, and A.T.C. and J.C.M. constructed and characterized the Δcsp1csp2 M. trichosporium OB3b strain. C.D. wrote the paper with help from all authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Christopher Dennison.

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https://doi.org/10.1038/nature14854

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