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Atomically defined mechanism for proton transfer to a buried redox centre in a protein

Nature volume 405, pages 814–817 (2000)Cite this article

An Erratum to this article was published on 07 September 2000

Abstract

The basis of the chemiosmotic theory is that energy from light or respiration is used to generate a trans-membrane proton gradient1. This is largely achieved by membrane-spanning enzymes known as ‘proton pumps’2,3,4,5. There is intense interest in experiments which reveal, at the molecular level, how protons are drawn through proteins6,7,8,9,10,11,12,13.Here we report the mechanism, at atomic resolution, for a single long-range electron-coupled proton transfer. In Azotobacter vinelandii ferredoxin I, reduction of a buried iron–sulphur cluster draws in a solvent proton, whereas re-oxidation is ‘gated’ by proton release to the solvent. Studies of this ‘proton-transferring module’ by fast-scan protein film voltammetry, high-resolution crystallography, site-directed mutagenesis and molecular dynamics, reveal that proton transfer is exquisitely sensitive to the position and pK of a single amino acid. The proton is delivered through the protein matrix by rapid penetrative excursions of the side-chain carboxylate of a surface residue (Asp 15), whose pK shifts in response to the electrostatic charge on the iron–sulphur cluster. Our analysis defines the structural, dynamic and energetic requirements for proton courier groups in redox-driven proton-pumping enzymes.

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Figure 1: The residues in the vicinity of the [3Fe–4S] cluster in oxidized native Azotobacter vinelandii Ferredoxin I, taken from coordinates 7FD1.
Figure 2: Structures of the various mutant forms of FdI in the region of interest, compared with the structure of oxidized native FdI.
Figure 3: Movement of the Asp15 side chain during redox-driven proton transfers.

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Acknowledgements

We thank T. Poulos and J. Lanyi for comments on the manuscript. This research was supported by grants from the NIH, EPSRC, and BBRSC. B.B.K. thanks The Fulbright Commission for a Senior Scholarship, and the John Simon Guggenheim Foundation for a Travelling Fellowship. R.C. is grateful to The National Council of Science and Technology of Mexico (CONACYT) for their support.

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Author notes

  1. Judy Hirst

    Present address: Medical Research Council Dunn Human Nutrition Unit, Hills Road, Cambridge, CB2 2XY, UK

  2. Kaisheng Chen, Judy Hirst and Raul Camba: These authors contributed equally to this work

Authors and Affiliations

  1. Department of Molecular Biology and Biochemistry, University of California, Irvine, 92612, California, USA

    Kaisheng Chen, Christopher A. Bonagura & Barbara. K. Burgess

  2. Department of Chemistry, Oxford University, Oxford, OX1 3QR, UK

    Judy Hirst, Raul Camba & Fraser A. Armstrong

  3. Department of Molecular Biology The Scripps Research Institute, 10550 North Torrey Pines Road , La Jolla, 92037-1083, California, USA

    C. David Stout

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Correspondence to Fraser A. Armstrong.

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Chen, K., Hirst, J., Camba, R. et al. Atomically defined mechanism for proton transfer to a buried redox centre in a protein. Nature 405, 814–817 (2000). https://doi.org/10.1038/35015610

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