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The Crystal Structure of the Apoenzyme of the Iron-Sulphur Cluster-free Hydrogenase

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Mamat,  Björn
Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max Planck Society;
Max-Planck-Institut für terrestrische Mikrobiologie, 35043 Marburg, Germany;

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

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

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Citation

Pilak, O., Mamat, B., Vogt, S., Hagemeier, C. H., Thauer, R. K., Shima, S., et al. (2006). The Crystal Structure of the Apoenzyme of the Iron-Sulphur Cluster-free Hydrogenase. Journal of Molecular Biology (London), 358(3), 798-809. doi:10.1016/j.jmb.2006.02.035.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0024-D922-9
Abstract
The iron–sulphur cluster-free hydrogenase (Hmd, EC 1.12.98.2) from methanogenic archaea is a novel type of hydrogenase that tightly binds an iron-containing cofactor. The iron is coordinated by two CO molecules, one sulphur and a pyridone derivative, which is linked via a phosphodiester bond to a guanosine base. We report here on the crystal structure of the Hmd apoenzyme from Methanocaldococcus jannaschii at 1.75 Å and from Methanopyrus kandleri at 2.4 Å resolution. Homodimeric Hmd reveals a unique architecture composed of one central and two identical peripheral globular units. The central unit is composed of the intertwined C-terminal segments of both subunits, forming a novel intersubunit fold. The two peripheral units consist of the N-terminal domain of each subunit. The Rossmann fold-like structure of the N-terminal domain contains a mononucleotide-binding site, which could harbour the GMP moiety of the cofactor. Another binding site for the iron-containing cofactor is most probably Cys176, which is located at the bottom of a deep intersubunit cleft and which has been shown to be essential for enzyme activity. Adjacent to the iron of the cofactor modelled as a ligand to Cys176, an extended U-shaped extra electron density, interpreted as a polyethyleneglycol fragment, suggests a binding site for the substrate methenyltetrahydromethanopterin.