title: De novo modeling of the F(420)-reducing [NiFe]-hydrogenase from a methanogenic archaeon by cryo-electron microscopy.
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.
authors.affiliation: Department of Structural Biology , Max Planck Institute of Biophysics , Frankfurt , Germany.
authors.forename: Deryck J
authors.initials: DJ
authors.lastname: Mills
authors.forename: Stella
authors.initials: S
authors.lastname: Vitt
authors.forename: Mike
authors.initials: M
authors.lastname: Strauss
authors.forename: Seigo
authors.initials: S
authors.lastname: Shima
authors.forename: Janet
authors.initials: J
authors.lastname: Vonck
mesh_terms: D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure; D001665:Binding Sites; D020285:Cryoelectron Microscopy; D006864:Hydrogenase / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure; D017013:Methanobacteriaceae / Q000145:classification / Q000201:enzymology* / Q000648:ultrastructure; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010084:Oxidation-Reduction; D011485:Protein Binding; D020836:Protein Structure, Quaternary; D012256:Riboflavin / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism
chemical_list: D019843:Archaeal Proteins; C015084:coenzyme F420; C043296:nickel-iron hydrogenase; D006864:Hydrogenase; D012256:Riboflavin
keywords: Methanothermobacter marburgensis; Other; cryo-electron microscopy; hydrogenase; methanogenesis