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De novo modeling of the F420-reducing [NiFe]-hydrogenase from a methanogenic archaeon by cryo-electron microscopy

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Mills,  Deryck J.
Department of Structural Biology, Max Planck Institute of Biophysics, Max Planck Society;

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Vitt,  Stella
Max Planck Institute for terrestrial Microbiology, Max Planck Society;

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Strauss,  Mike
Department of Structural Biology, Max Planck Institute of Biophysics, Max Planck Society;

Shima,  Seigo
Max Planck Institute for terrestrial Microbiology, Max Planck Society;
Japan Science and Technology Agency Kawaguchi, Japan;

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Vonck,  Janet
Department of Structural Biology, Max Planck Institute of Biophysics, Max Planck Society;

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Citation

Mills, D. J., Vitt, S., Strauss, M., Shima, S., & Vonck, J. (2013). De novo modeling of the F420-reducing [NiFe]-hydrogenase from a methanogenic archaeon by cryo-electron microscopy. eLife, 2: e00218. doi:10.7554/eLife.00218.


Cite as: https://hdl.handle.net/11858/00-001M-0000-0024-D509-3
Abstract
Methanogenic archaea use a [NiFe]-hydrogenase, Frh, for oxidation/reduction of F420, an important hydride carrier in the methanogenesis pathway from H2 and CO2. Frh accounts for about 1% of the cytoplasmic protein and forms a huge complex consisting of FrhABG heterotrimers with each a [NiFe] center, four Fe-S clusters and an FAD. Here, we report the structure determined by near-atomic resolution cryo-EM of Frh with and without bound substrate F420. The polypeptide chains of FrhB, for which there was no homolog, was traced de novo from the EM map. The 1.2-MDa complex contains 12 copies of the heterotrimer, which unexpectedly form a spherical protein shell with a hollow core. The cryo-EM map reveals strong electron density of the chains of metal clusters running parallel to the protein shell, and the F420-binding site is located at the end of the chain near the outside of the spherical structure.