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Insights into the Molecular Mechanism of Formaldehyde Inhibition of [FeFe]-Hydrogenases

  • Jifu Duan*
    Jifu Duan
    Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
    *Email: [email protected]
    More by Jifu Duan
  • Astrit Veliju
    Astrit Veliju
    Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
  • Oliver Lampret
    Oliver Lampret
    Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
  • Lingling Liu
    Lingling Liu
    Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
    More by Lingling Liu
  • Shanika Yadav
    Shanika Yadav
    Inorganic Chemistry I, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
  • Ulf-Peter Apfel
    Ulf-Peter Apfel
    Inorganic Chemistry I, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
    Department of Energy, Electrosynthesis Group, Fraunhofer UMSICHT, 46047 Oberhausen, Germany
  • Fraser A. Armstrong
    Fraser A. Armstrong
    Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
  • Anja Hemschemeier
    Anja Hemschemeier
    Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
  • , and 
  • Eckhard Hofmann
    Eckhard Hofmann
    Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
Cite this: J. Am. Chem. Soc. 2023, 145, 48, 26068–26074
Publication Date (Web):November 20, 2023
https://doi.org/10.1021/jacs.3c07800
Copyright © 2023 American Chemical Society

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    Abstract

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    [FeFe]-hydrogenases are efficient H2 converting biocatalysts that are inhibited by formaldehyde (HCHO). The molecular mechanism of this inhibition has so far not been experimentally solved. Here, we obtained high-resolution crystal structures of the HCHO-treated [FeFe]-hydrogenase CpI from Clostridium pasteurianum, showing HCHO reacts with the secondary amine base of the catalytic cofactor and the cysteine C299 of the proton transfer pathway which both are very important for catalytic turnover. Kinetic assays via protein film electrochemistry show the CpI variant C299D is significantly less inhibited by HCHO, corroborating the structural results. By combining our data from protein crystallography, site-directed mutagenesis and protein film electrochemistry, a reaction mechanism involving the cofactor’s amine base, the thiol group of C299 and HCHO can be deduced. In addition to the specific case of [FeFe]-hydrogenases, our study provides additional insights into the reactions between HCHO and protein molecules.

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    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/jacs.3c07800.

    • Materials and methods; reaction schemes of HCHO with protein amines or thiols; structural details of 8QM3 and 8PVM; protein film electrochemistry results; reaction mechanisms of [FeFe]-hydrogenases with HCHO; crystallographic statistics of PDB 8QM3 and 8PVM; PCR primers for generating expression construct of CpI-C39S-C184A; phenotypes of different [FeFe]-hydrogenases under H2 production and oxidation conditions in terms of HCHO inhibition (PDF)

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