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Structural insights into electron transfer in caa3-type cytochrome oxidase

Nature volume 487, pages 514–518 (2012)Cite this article

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Abstract

Cytochrome c oxidase is a member of the haem copper oxidase superfamily (HCO)1. HCOs function as the terminal enzymes in the respiratory chain of mitochondria and aerobic prokaryotes, coupling molecular oxygen reduction to transmembrane proton pumping. Integral to the enzyme’s function is the transfer of electrons from cytochrome c to the oxidase via a transient association of the two proteins. Electron entry and exit are proposed to occur from the same site on cytochrome c2,3,4. Here we report the crystal structure of the caa3-type cytochrome oxidase from Thermus thermophilus, which has a covalently tethered cytochrome c domain. Crystals were grown in a bicontinuous mesophase using a synthetic short-chain monoacylglycerol as the hosting lipid. From the electron density map, at 2.36 Å resolution, a novel integral membrane subunit and a native glycoglycerophospholipid embedded in the complex were identified. Contrary to previous electron transfer mechanisms observed for soluble cytochrome c, the structure reveals the architecture of the electron transfer complex for the fused cupredoxin/cytochrome c domain, which implicates different sites on cytochrome c for electron entry and exit. Support for an alternative to the classical proton gate characteristic of this HCO class is presented.

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Figure 1: Structure of and cofactor arrangement in caa 3 -oxidase.
Figure 2: Active site, water pool and oxygen channel in caa 3 -oxidase.
Figure 3: Proton pathways in caa 3 -oxidase.
Figure 4: Cytochrome c /cupredoxin complex and electron transfer pathway in caa 3 -oxidase.

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Protein Data Bank

Data deposits

Coordinates and structure factors for caa3-oxidase are deposited in the Protein Data Bank (accession code 2YEV).

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Acknowledgements

We acknowledge support from Science Foundation Ireland Grants 07/IN.1/B1836 (M.C.) and BICF685 (T.S.), the National Institutes of Health Grants GM75915, P50GM073210, U54GM094599 (M.C.), and FP7 COST CM0902 (M.C.) and Marie Curie Actions PIEF-GA-2009-235612 (D.A.). We thank D. Hart, J. Lee and T. Smyth for help with 7.7 MAG synthesis, M. Dewor for amino acid sequencing, C. Soares for discussions regarding surface potential calculations, and G. Winter for help with data reduction from multiple crystals. The assistance and support of beamline scientists at the Advanced Photon Source (23-ID), Diamond Light Source (I24) and Swiss Light Source (PX1) are gratefully acknowledged.

Author information

Authors and Affiliations

  1. Department of Chemical and Environmental Sciences, University of Limerick, Limerick, Ireland

    Joseph A. Lyons, Orla Slattery & Tewfik Soulimane

  2. School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland

    Joseph A. Lyons, David Aragão & Martin Caffrey

  3. Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia,

    David Aragão

  4. Theoretical Biochemistry Laboratory, RIKEN Advanced Science Institute, Wako, Saitama 351-0198, Japan,

    Andrei V. Pisliakov

  5. Materials and Surface Science Institute, University of Limerick, Limerick, Ireland

    Tewfik Soulimane

  6. School of Medicine, Trinity College Dublin, Dublin, Ireland

    Martin Caffrey

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  1. Joseph A. Lyons
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Contributions

J.A.L. synthesized 7.7 MAG, optimized crystallization conditions, collected and processed data, solved, refined and analysed the structure, and wrote the manuscript. D.A. collected crystals, collected and processed data, solved, refined and analysed the structure, and wrote the manuscript. O.S. performed initial protein production, purification, crystallization and data collection. A.V.P. carried out molecular dynamics simulations and pKa calculations. T.S. initiated the project, produced, purified and characterized protein, helped with crystallization, data collection and processing and structure analysis, and wrote the manuscript. M.C. was responsible for the overall project strategy and management and oversaw manuscript preparation.

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Correspondence to Tewfik Soulimane or Martin Caffrey.

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The authors declare no competing financial interests.

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Lyons, J., Aragão, D., Slattery, O. et al. Structural insights into electron transfer in caa3-type cytochrome oxidase. Nature 487, 514–518 (2012). https://doi.org/10.1038/nature11182

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