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The atomic-resolution crystal structure of activated [Fe]-hydrogenase

Nature Catalysis volume 2, pages 537–543 (2019)Cite this article

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Abstract

Hydrogenases are promising templates for constructing new H2-based catalysts. [Fe]-hydrogenase, which features an iron-guanylylpyridinol (FeGP) cofactor, catalyses a reversible hydride transfer from H2 to methenyl-tetrahydromethanopterin (methenyl-H4MPT+, a C1 carrier in methanogens). Here, we present a detailed mechanistic scenario of this reaction based on the 1.06 Å resolution structure of [Fe]-hydrogenase in a closed active form, in which the Fe of the FeGP cofactor is positioned near the hydride-accepting C14a of a remarkably distorted methenyl-H4MPT+. The open-to-closed transition generates an unsaturated pentacoordinated Fe on expulsion of a water ligand. Quantum mechanics/molecular mechanics computations based on experimental models indicate that a deprotonated 2-OH group on the FeGP cofactor acts as a catalytic base and provides a fairly complete picture of H2 activation: H2 binding on the empty Fe site was found to be nearly thermo-neutral while H2 cleavage and hydride transfer proceed smoothly. The overall reaction involves a repositioning and relaxation of the distorted methenyl-H4MPT+.

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Fig. 1: The catalytic reaction and chemical structures.
Fig. 2: Structures of the open and closed conformations of [Fe]-hydrogenase.
Fig. 3: Electron density map and model of the cofactor and substrate.
Fig. 4: The proposed catalytic cycle of [Fe]-hydrogenase.

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Data availability

The data that support the plots within this paper and other findings of this study are available from the corresponding authors on reasonable request. X-ray crystallographic data are available in the RCSB-Protein Data Bank under accession numbers 6HAC (open conformation), 6HAV (closed conformation form A) and 6HAE (closed conformation form B).

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Acknowledgements

This work was supported by grants from the Max Planck Society (to S.S., E.B. and U.E.), Deutsche Forschungsgemeinschaft (Iron-Sulfur for Life, SH 87/1-1 to S.S.) and the Swiss National Science Foundation (to X.H.). M.D.W. thanks C. Corminboeuf (École Polytechnique Fédérale de Lausanne, Switzerland) for financial support and the Laboratory for Computational Molecular Design (EPFL) for providing computing resources. The authors are grateful to H. Michel for continuous support and the staff of the PX II beamline at the Swiss Light Source (SLS) for help with data collection. The authors also thank the staff from the BM30A (FIP) beamline at the European Synchrotron Radiation Facility (ESRF). G.H. was supported by a fellowship from China Scholarship Council (CSC).

Author information

Author notes

  1. Tristan Wagner

    Present address: Microbial Metabolism group, Max Planck Institute for Marine Microbiology, Bremen, Germany

  2. These authors contributed equally: Gangfeng Huang, Tristan Wagner.

Authors and Affiliations

  1. Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany

    Gangfeng Huang, Tristan Wagner & Seigo Shima

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

    Matthew D. Wodrich & Xile Hu

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

    Matthew D. Wodrich

  4. Department of Physics, Freie Universität Berlin, Berlin, Germany

    Kenichi Ataka

  5. Department Molecular Theory and Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany

    Eckhard Bill

  6. Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany

    Ulrich Ermler

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Contributions

S.S. directed and designed research. G.H. performed cultivation, enzyme purification and crystallization. T.W. and U.E. collected X-ray data. T.W. solved, refined and deposited the structure. M.D.W. and X.H. performed and analysed the QM/MM computations. K.A. performed infrared spectroscopy and E.B. performed Mössbauer spectroscopy. All authors contributed to writing the paper.

Corresponding author

Correspondence to Seigo Shima.

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Supplementary Information

Supplementary Information

Supplementary Methods, Supplementary Figs. 1–15, Supplementary Tables 1–3, Supplementary references

Reporting Summary

Supplementary Data 1

Structure 2

Supplementary Data 2

Structure 3

Supplementary Data 3

Structure 4

Supplementary Data 4

Structure 5

Supplementary Data 5

TS3,4

Supplementary Data 6

TS4,5

Supplementary Video 1

Open/closed conformational change

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Huang, G., Wagner, T., Wodrich, M.D. et al. The atomic-resolution crystal structure of activated [Fe]-hydrogenase. Nat Catal 2, 537–543 (2019). https://doi.org/10.1038/s41929-019-0289-4

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