3ZFS

Cryo-EM structure of the F420-reducing NiFe-hydrogenase from a methanogenic archaeon with bound substrate

Summary for 3ZFS

• Entry DOI: 10.2210/pdb3zfs/pdb
• EMDB information: 2097
• Descriptor: F420-REDUCING HYDROGENASE, SUBUNIT ALPHA, F420-REDUCING HYDROGENASE, SUBUNIT GAMMA, F420-REDUCING HYDROGENASE, SUBUNIT BETA, ... (9 entities in total)
• Functional Keywords: oxidoreductase, methanogenesis
• Biological source: METHANOTHERMOBACTER MARBURGENSIS; More
• Total number of polymer chains: 3
• Total formula weight: 109135.98

Authors

Mills, D.J.,Vitt, S.,Strauss, M.,Shima, S.,Vonck, J. (deposition date: 2012-12-12, release date: 2013-03-06, Last modification date: 2024-05-08)

Primary citation

Mills, D.J.,Vitt, S.,Strauss, M.,Shima, S.,Vonck, J.
De Novo Modeling of the F420-Reducing [Nife]-Hydrogenase from a Methanogenic Archaeon by Cryo-Electron Microscopy
Elife, 2:218-, 2013

PubMed 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. DOI:http://dx.doi.org/10.7554/eLife.00218.001.

PubMed: 23483797
DOI: 10.7554/ELIFE.00218

Experimental method

ELECTRON MICROSCOPY (4 Å)