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Reconstitution of [Fe]-hydrogenase using model complexes

Nature Chemistry volume 7, pages 995–1002 (2015)Cite this article

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Abstract

[Fe]-Hydrogenase catalyses the reversible hydrogenation of a methenyltetrahydromethanopterin substrate, which is an intermediate step during the methanogenesis from CO2 and H2. The active site contains an iron-guanylylpyridinol cofactor, in which Fe2+ is coordinated by two CO ligands, as well as an acyl carbon atom and a pyridinyl nitrogen atom from a 3,4,5,6-substituted 2-pyridinol ligand. However, the mechanism of H2 activation by [Fe]-hydrogenase is unclear. Here we report the reconstitution of [Fe]-hydrogenase from an apoenzyme using two FeGP cofactor mimics to create semisynthetic enzymes. The small-molecule mimics reproduce the ligand environment of the active site, but are inactive towards H2 binding and activation on their own. We show that reconstituting the enzyme using a mimic that contains a 2-hydroxypyridine group restores activity, whereas an analogous enzyme with a 2-methoxypyridine complex was essentially inactive. These findings, together with density functional theory computations, support a mechanism in which the 2-hydroxy group is deprotonated before it serves as an internal base for heterolytic H2 cleavage.

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Figure 1: Reaction catalysed by [Fe]-hydrogenase and reconstitution of [Fe]-hydrogenase with the model complexes of the FeGP cofactor.
Figure 2: Structures of synthetic models of the FeGP cofactor.
Figure 3: Infrared spectra of the model complexes and FeGP cofactor.
Figure 4: Activity of the [Fe]-hydrogenase holoenzyme reconstituted with model compound 3i.
Figure 5: Infrared spectra of the [Fe]-hydrogenases reconstituted with 3i and 4i.
Figure 6: Lowest-energy reaction pathways for the catalytic cycles that involve model complexes 5 and 6.

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Acknowledgements

We thank R. Thauer for discussions and helpful suggestions. C. Corminboeuf and the Laboratory for Computational Molecular Design at the EPFL are acknowledged for providing computational resources. This work was supported by grants from the Max Planck Society (to R. Thauer) and for the PRESTO program from the Japan Science and Technology Agency to S. Shima, a grant from the National Natural Science Foundation of China (No. 21302028) to D. Chen and grants from the Swiss National Science Foundation (200020_134473/1 and 200020_152850/1) to X. Hu.

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Authors and Affiliations

  1. Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany

    Seigo Shima, Takashi Fujishiro & Jörg Kahnt

  2. PRESTO, Japan Science and Technology Agency (JST), Saitama, 332-0012, Japan

    Seigo Shima

  3. School of Chemical Engineering and Technology, Harbin Institute of Technology, Harbin, 150001, China

    Dafa Chen

  4. Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Science and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland

    Tao Xu, Matthew D. Wodrich, Katherine M. Schultz & Xile Hu

  5. Laboratory for Computational Molecular Design, Institute of Chemical Science and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland

    Matthew D. Wodrich

  6. Department of Physics, Freie Universität Berlin, Berlin, 14195, Germany

    Kenichi Ataka

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Contributions

S.S. and X.H. directed the research. S.S., D.C. and X.H. designed the study. D.C., T.X. and K.M.S. synthesized the model compounds. S.S. reconstituted and characterized the semisynthetic [Fe]-hydrogenase. J.K. performed the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis. K.A. performed the infrared spectroscopy with S.S. and T.F. M.D.W. carried out the computations. S.S. and X.H. wrote the manuscript with contributions from all the co-authors.

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Correspondence to Seigo Shima or Xile Hu.

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Shima, S., Chen, D., Xu, T. et al. Reconstitution of [Fe]-hydrogenase using model complexes. Nature Chem 7, 995–1002 (2015). https://doi.org/10.1038/nchem.2382

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