3zfs Citations

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

OpenAccess logo Elife 2 e00218 (2013)
Cited: 18 times
EuropePMC logo PMID: 23483797

Abstract

Methanogenic archaea use a [NiFe]-hydrogenase, Frh, for oxidation/reduction of F, an important hydride carrier in the methanogenesis pathway from H and CO. 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 F. 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 F-binding site is located at the end of the chain near the outside of the spherical structure. http://dx.doi.org/10.7554/eLife.00218.001.

Reviews citing this publication (6)

  1. Bioenergetics and anaerobic respiratory chains of aceticlastic methanogens. Welte C, Deppenmeier U. Biochim. Biophys. Acta 1837 1130-1147 (2014)
  2. Invited review article: Methods for imaging weak-phase objects in electron microscopy. Glaeser RM. Rev Sci Instrum 84 111101 (2013)
  3. Opportunities and challenges for time-resolved studies of protein structural dynamics at X-ray free-electron lasers. Neutze R. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 369 20130318 (2014)
  4. Bioenergetics and anaerobic respiratory chains of aceticlastic methanogens. Welte C, Deppenmeier U. Biochim. Biophys. Acta 1837 1130-1147 (2014)
  5. Opportunities and challenges for time-resolved studies of protein structural dynamics at X-ray free-electron lasers. Neutze R. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 369 20130318 (2014)
  6. Invited review article: Methods for imaging weak-phase objects in electron microscopy. Glaeser RM. Rev Sci Instrum 84 111101 (2013)

Articles citing this publication (12)

  1. Horizontal membrane-intrinsic α-helices in the stator a-subunit of an F-type ATP synthase. Allegretti M, Klusch N, Mills DJ, Vonck J, Kühlbrandt W, Davies KM. Nature 521 237-240 (2015)
  2. Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector. Allegretti M, Mills DJ, McMullan G, Kühlbrandt W, Vonck J. Elife 3 e01963 (2014)
  3. Structure of β-galactosidase at 3.2-Å resolution obtained by cryo-electron microscopy. Bartesaghi A, Matthies D, Banerjee S, Merk A, Subramaniam S. Proc. Natl. Acad. Sci. U.S.A. 111 11709-11714 (2014)
  4. Avoiding the pitfalls of single particle cryo-electron microscopy: Einstein from noise. Henderson R. Proc. Natl. Acad. Sci. U.S.A. 110 18037-18041 (2013)
  5. De novo protein structure determination from near-atomic-resolution cryo-EM maps. Wang RY, Kudryashev M, Li X, Egelman EH, Basler M, Cheng Y, Baker D, DiMaio F. Nat. Methods 12 335-338 (2015)
  6. Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival. Greening C, Biswas A, Carere CR, Jackson CJ, Taylor MC, Stott MB, Cook GM, Morales SE. ISME J 10 761-777 (2016)
  7. Direct detection pays off for electron cryo-microscopy. Grigorieff N. Elife 2 e00573 (2013)
  8. The F₄₂₀-reducing [NiFe]-hydrogenase complex from Methanothermobacter marburgensis, the first X-ray structure of a group 3 family member. Vitt S, Ma K, Warkentin E, Moll J, Pierik AJ, Shima S, Ermler U. J. Mol. Biol. 426 2813-2826 (2014)
  9. Electron microscopy analysis of a disaccharide analog complex reveals receptor interactions of adeno-associated virus. Xie Q, Spilman M, Meyer NL, Lerch TF, Stagg SM, Chapman MS. J. Struct. Biol. 184 129-135 (2013)
  10. Crystal Structure and Catalytic Mechanism of 7-Hydroxymethyl Chlorophyll a Reductase. Wang X, Liu L. J. Biol. Chem. 291 13349-13359 (2016)
  11. Functional asymmetry and electron flow in the bovine respirasome. Sousa JS, Mills DJ, Vonck J, Kühlbrandt W. Elife 5 (2016)
  12. Towards artificial methanogenesis: biosynthesis of the [Fe]-hydrogenase cofactor and characterization of the semi-synthetic hydrogenase. Bai L, Fujishiro T, Huang G, Koch J, Takabayashi A, Yokono M, Tanaka A, Xu T, Hu X, Ermler U, Shima S. Faraday Discuss. 198 37-58 (2017)