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TitleDe novo modeling of the F(420)-reducing [NiFe]-hydrogenase from a methanogenic archaeon by cryo-electron microscopy.
Journal, issue, pagesElife, Vol. 2, Page e00218, Year 2013
Publish dateMar 5, 2013
AuthorsDeryck J Mills / Stella Vitt / Mike Strauss / Seigo Shima / Janet Vonck /
PubMed AbstractMethanogenic 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 ...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.
External linksElife / PubMed:23483797 / PubMed Central
MethodsEM (single particle)
Resolution4 - 4.5 Å
Structure data

2096

3zfs

EMDB-2096: Cryo-EM structure of the F420-reducing [NiFe]-hydrogenase from a methanogenic archaeon at near-atomic resolution
PDB-3zfs: Cryo-EM structure of the F420-reducing NiFe-hydrogenase from a methanogenic archaeon with bound substrate
Method: EM (single particle) / Resolution: 4.5 Å

2097

3zfs

EMDB-2097: Cryo-EM structure of the F420-reducing [NiFe]-hydrogenase from a methanogenic archaeon with bound substrate
PDB-3zfs: Cryo-EM structure of the F420-reducing NiFe-hydrogenase from a methanogenic archaeon with bound substrate
Method: EM (single particle) / Resolution: 4.5 Å

Chemicals

ChemComp-FCO:
CARBONMONOXIDE-(DICYANO) IRON

ChemComp-NI:
NICKEL (II) ION

ChemComp-FE2:
Unknown entry

ChemComp-SF4:
IRON/SULFUR CLUSTER

ChemComp-F42:
COENZYME F420

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

Source
  • methanothermobacter marburgensis (archaea)
KeywordsOXIDOREDUCTASE / METHANOGENESIS

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