5XF9

Crystal structure of NAD+-reducing [NiFe]-hydrogenase in the air-oxidized state

Summary for 5XF9

• Entry DOI: 10.2210/pdb5xf9/pdb
• Related: 5XFA
• Descriptor: NAD-reducing hydrogenase, MAGNESIUM ION, FLAVIN MONONUCLEOTIDE, ... (11 entities in total)
• Functional Keywords: hydrogenase, ni-fe, fe-s, oxidoreductase
• Biological source: Hydrogenophilus thermoluteolus; More
• Total number of polymer chains: 8
• Total formula weight: 331217.72

Authors

Shomura, Y.,Taketa, M.,Nakashima, H.,Tai, H.,Nakagawa, H.,Ikeda, Y.,Ishii, M.,Igarashi, Y.,Nishihara, H.,Yoon, K.S.,Ogo, S.,Hirota, S.,Higuchi, Y. (deposition date: 2017-04-09, release date: 2017-08-23, Last modification date: 2024-10-16)

Primary citation

Shomura, Y.,Taketa, M.,Nakashima, H.,Tai, H.,Nakagawa, H.,Ikeda, Y.,Ishii, M.,Igarashi, Y.,Nishihara, H.,Yoon, K.S.,Ogo, S.,Hirota, S.,Higuchi, Y.
Structural basis of the redox switches in the NAD(+)-reducing soluble [NiFe]-hydrogenase
Science, 357:928-932, 2017

PubMed 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 O 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.

PubMed: 28860386
DOI: 10.1126/science.aan4497

Experimental method

X-RAY DIFFRACTION (2.58 Å)