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Deciphering the oxygen activation mechanism at the CuC site of particulate methane monooxygenase

Abstract

The enzymatic oxidation of methane to methanol was discovered in methanotrophs over 110 years ago. Nevertheless, the mechanism of action of particulate methane monooxygenase (pMMO) remains elusive, especially regarding O2 activation and the nature of the active species of the enzyme. Here we decipher the catalytic cycle of pMMO in the presence of the physiological reductant duroquinol (DQH2). We demonstrate that O2 activation is in fact initiated by a CuC(ii)–DQH species generated by deprotonation of DQH2. Our simulations capture the exclusive pathway for the sequential formation of the intermediates, CuC(ii)−O2•−, CuC(ii)−OOH and H2O2, along the O2 reduction pathway. Furthermore, H2O2 activation by CuC(ii)−DQH is initiated by dissociation of DQH to yield CuC(i), followed by CuC(i)-catalysed O−O homolysis, en route to the formation of the CuC(ii)−O•− species, which is responsible for C−H oxidations. These findings uncover the important roles of the phenol co-substrate for O2 activation and help resolve the enigmatic mechanism of pMMO.

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Fig. 1: Structures of pMMO and quinol reductants.
Fig. 2: Possible mechanisms for reduction of the CuC(ii) site by co-substrate DQH2.
Fig. 3: The calculated mechanism of O2 reduction by CuC(ii)–DQH.
Fig. 4: The calculated mechanisms of H2O2 formation and its conversion to CuC(ii)−O.
Fig. 5: A proposed full catalytic cycle of pMMO in the presence of DQH2.

Data availability

The authors declare that all the data supporting the findings of this work are available within the article and its Supplementary Information, Supplementary Data or from the corresponding authors upon request.

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Acknowledgements

We thank B. M. Hoffman for helpful discussions. B. W. is grateful for financial support from National Natural Science Foundation of China (nos. 21933009 and 22073077). S.S. thanks the Israel Science Foundation for support (grant ISF 520/18).

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B.W. and W.P. conceived and designed the project. W.P. conducted the computational studies and made all figures, with X.Q. providing assistance. All authors participated in the discussion, and W.P., B.W. and S.S. co-wrote the manuscript.

Corresponding authors

Correspondence to Sason Shaik or Binju Wang.

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The authors declare no competing interests.

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Peer review information Nature Catalysis thanks Jeewon Lee, Lou Noodleman and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Methods, Table 1, Figs. 1–28, Notes 1−4 and References.

Supplementary Data 1

The Cartesian coordinates of the truncated PDB (solvation waters 3 Å away from the protein are removed) of all species involved in the catalytic cycle (Fig. 5) from QM/MM metadynamics.

Supplementary Data 2

The Cartesian coordinates of all computed species in QM calculations.

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Peng, W., Qu, X., Shaik, S. et al. Deciphering the oxygen activation mechanism at the CuC site of particulate methane monooxygenase. Nat Catal 4, 266–273 (2021). https://doi.org/10.1038/s41929-021-00591-4

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