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The F420-Reducing [NiFe]-Hydrogenase Complex from Methanothermobacter marburgensis, the First X-ray Structure of a Group 3 Family Member

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Vitt,  Stella
Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany, Max Planck Society;

Ma,  Kesen
Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany, Max Planck Society;
Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, Canada N2L3G1;

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Warkentin,  Eberhard
Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max Planck Society;

Moll,  Johanna
Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany, Max Planck Society;

Pierik,  Antonio J.
Institute of Cytobiology, Philipps Universität Marburg, Robert-Koch Straße 6, 35037 Marburg, Germany;
Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany, Max Planck Society;

Shima,  Seigo
Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany, Max Planck Society;
PRESTO, Japan Science and Technology Agency, Honcho, Kawaguchi, Saitama 332-0012, Japan;

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Ermler,  Ulrich
Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max Planck Society;

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Citation

Vitt, S., Ma, K., Warkentin, E., Moll, J., Pierik, A. J., Shima, S., et al. (2014). The F420-Reducing [NiFe]-Hydrogenase Complex from Methanothermobacter marburgensis, the First X-ray Structure of a Group 3 Family Member. Journal of Molecular Biology (London), 426(15), 2813-2826. doi:10.1016/j.jmb.2014.05.024.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0026-B1A3-8
Abstract
The reversible redox reaction between coenzyme F420 and H2 to F420H2 is catalyzed by an F420-reducing [NiFe]-hydrogenase (FrhABG), which is an enzyme of the energy metabolism of methanogenic archaea. FrhABG is a group 3 [NiFe]-hydrogenase with a dodecameric quaternary structure of 1.25 MDa as recently revealed by high-resolution cryo-electron microscopy. We report on the crystal structure of FrhABG from Methanothermobacter marburgensis at 1.7 Å resolution and compare it with the structures of group 1 [NiFe]-hydrogenases, the only group structurally characterized yet. FrhA is similar to the large subunit of group 1 [NiFe]-hydrogenases regarding its core structure and the embedded [NiFe]-center but is different because of the truncation of ca 160 residues that results in similar but modified H2 and proton transport pathways and in suitable interfaces for oligomerization. The small subunit FrhG is composed of an N-terminal domain related to group 1 enzymes and a new C-terminal ferredoxin-like domain carrying the distal and medial [4Fe-4S] clusters. FrhB adopts a novel fold, binds one [4Fe-4S] cluster as well as one FAD in a U-shaped conformation and provides the F420-binding site at the Si-face of the isoalloxazine ring. Similar electrochemical potentials of both catalytic reactions and the electron-transferring [4Fe-4S] clusters, determined to be E°′ ≈ −400 mV, are in full agreement with the equalized forward and backward rates of the FrhABG reaction. The protein might contribute to balanced redox potentials by the aspartate coordination of the proximal [4Fe-4S] cluster, the new ferredoxin module and a rather negatively charged FAD surrounding.