Article | Published:

Structural insights into the bacterial carbon–phosphorus lyase machinery

Nature volume 525, pages 6872 (03 September 2015) | Download Citation

Abstract

Phosphorus is required for all life and microorganisms can extract it from their environment through several metabolic pathways. When phosphate is in limited supply, some bacteria are able to use phosphonate compounds, which require specialized enzymatic machinery to break the stable carbon–phosphorus (C–P) bond. Despite its importance, the details of how this machinery catabolizes phosphonates remain unknown. Here we determine the crystal structure of the 240-kilodalton Escherichia coli C–P lyase core complex (PhnG–PhnH–PhnI–PhnJ; PhnGHIJ), and show that it is a two-fold symmetric hetero-octamer comprising an intertwined network of subunits with unexpected self-homologies. It contains two potential active sites that probably couple phosphonate compounds to ATP and subsequently hydrolyse the C–P bond. We map the binding site of PhnK on the complex using electron microscopy, and show that it binds to a conserved insertion domain of PhnJ. Our results provide a structural basis for understanding microbial phosphonate breakdown.

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Electron Microscopy Data Bank

Protein Data Bank

Data deposits

Atomic coordinates and structure factors have been deposited in the Protein Data Bank (PDB) with accession code 4XB6. The EM density map has been deposited in the Electron Microscopy Data Bank (EMDB) with accession code EMD-3033.

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Acknowledgements

We are thankful to T. L. Sørensen at Diamond, T. Weinert at SLS as well as beamline staff at ESRF and MAX-Lab for help during X-ray data acquisition and S. Chen, C. G. Savva, J. Grimmett and T. Darling at the MRC-LMB for technical assistance with electron microscopy. This work was supported by the European Research Council grant no. 261151 (L.A.P.), MRC grant MC_U105192715 (L.A.P.), and the Danish National Research Foundation ‘Centre for mRNP biogenesis and metabolism’ (D.E.B.).

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Affiliations

  1. Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, DK-8000 Aarhus C, Denmark

    • Paulina Seweryn
    • , Lan Bich Van
    • , Morten Kjeldgaard
    • , Bjarne Hove-Jensen
    • , Bjarne Jochimsen
    •  & Ditlev E. Brodersen
  2. Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK

    • Christopher J. Russo
    •  & Lori A. Passmore

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Contributions

P.S., L.A.P., B.H.J., B.J. and D.E.B. designed and P.S., L.B.V., C.J.R. and B.J. carried out the experiments. P.S., M.K. and D.E.B. determined the crystal and EM structures while C.J.R. and L.A.P. carried out final refinement of the EM structure as well as EM structure validation. P.S., M.K., C.J.R., L.A.P., B.H.J., B.J. and D.E.B. wrote the manuscript.

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The authors declare no competing financial interests.

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Correspondence to Ditlev E. Brodersen.

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https://doi.org/10.1038/nature14683

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