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Structural basis of the redox switches in the NAD+-reducing soluble [NiFe]-hydrogenase

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Science  01 Sep 2017:
Vol. 357, Issue 6354, pp. 928-932
DOI: 10.1126/science.aan4497

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How a hydrogenase protects its active site

Hydrogen-metabolizing organisms use an [NiFe]-hydrogenase to catalyze hydrogen oxidation. One type of [NiFe]-hydrogenase, the NAD+-reducing soluble [NiFe]-hydrogenase (SH), couples reduction of NAD+ to the oxidation of hydrogen. Shomura et al. solved the structure of SH from an H2-oxidizing bacterium in both the air-oxidized and the active reduced state. In the reduced state, the NiFe catalytic center in SH has the same ligand coordination as in other [NiFe]-hydrogenases. However, the air-oxidized active site has an unusual coordination geometry that would prevent O2 from accessing the site and so may protect against irreversible oxidation.

Science, this issue p. 928

Abstract

NAD+ (oxidized form of NAD:nicotinamide adenine dinucleotide)–reducing soluble [NiFe]-hydrogenase (SH) is phylogenetically related to NADH (reduced form of NAD+):quinone oxidoreductase (complex I), but the geometrical arrangements of the subunits and Fe–S clusters are unclear. Here, we describe the crystal structures of SH in the oxidized and reduced states. The cluster arrangement is similar to that of complex I, but the subunits orientation is not, which supports the hypothesis that subunits evolved as prebuilt modules. The oxidized active site includes a six-coordinate Ni, which is unprecedented for hydrogenases, whose coordination geometry would prevent O2 from approaching. In the reduced state showing the normal active site structure without a physiological electron acceptor, the flavin mononucleotide cofactor is dissociated, which may be caused by the oxidation state change of nearby Fe–S clusters and may suppress production of reactive oxygen species.

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