DOI: 10.7554/elife.00218. De novo modeling of the F420-reducing [NiFe]-hydrogenase from a methanogenic archaeon by cryo-electron microscopy

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

10.7554/elife.00218

Crossref journal-article

eLife Sciences Publications, Ltd

eLife (4374)

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.

Bibliography

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. CLOCKSS.

Authors 5

Deryck J Mills (first)
Stella Vitt (additional)
Mike Strauss (additional)
Seigo Shima (additional)
Janet Vonck (additional)

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Dates

Type	When
Created	12 years, 5 months ago (March 5, 2013, 8:25 a.m.)
Deposited	1 year, 10 months ago (Oct. 11, 2023, 8:39 p.m.)
Indexed	1 week, 3 days ago (Aug. 19, 2025, 6:16 a.m.)
Issued	12 years, 5 months ago (March 5, 2013)
Published	12 years, 5 months ago (March 5, 2013)
Published Online	12 years, 5 months ago (March 5, 2013)

Funders 4

Max Planck Society
PRESTO program, Japan Science and Technology Agency (JST)
Max-Planck-Gesellschaft 10.13039/501100004189
Region: Europe
gov (Research institutes and centers)
Labels4
1. Max Planck Society for the Advancement of Science
2. Max-Planck-Gesellschaft zur Förderung der Wissenschaften
3. Max Planck Society
4. MPG
Japan Science and Technology Agency 10.13039/501100002241
Region: Asia
gov (National government)
Labels7
1. SCIENCE AND TECHNOLOGY AGENCY OF JAPAN
2. 国立研究開発法人科学技術振興機構
3. 国立研究開発法人科学技術振興機構 japan science and technology agency
4. Japan Science and Technology Agency (JST)
5. かがくぎじゅつしんこうきこう
6. 科学技術振興機構
7. JST

BibTeX

@article{Mills_2013, title={De novo modeling of the F420-reducing [NiFe]-hydrogenase from a methanogenic archaeon by cryo-electron microscopy}, volume={2}, ISSN={2050-084X}, url={http://dx.doi.org/10.7554/elife.00218}, DOI={10.7554/elife.00218}, journal={eLife}, publisher={eLife Sciences Publications, Ltd}, author={Mills, Deryck J and Vitt, Stella and Strauss, Mike and Shima, Seigo and Vonck, Janet}, year={2013}, month=mar }

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