title: Molecular evolution of gas cavity in [NiFeSe] hydrogenases resurrected in silico.
abstract: Oxygen tolerance of selenium-containing [NiFeSe] hydrogenases (Hases) is attributable to the high reducing power of the selenocysteine residue, which sustains the bimetallic Ni-Fe catalytic center in the large subunit. Genes encoding [NiFeSe] Hases are inherited by few sulphate-reducing δ-proteobacteria globally distributed under various anoxic conditions. Ancestral sequences of [NiFeSe] Hases were elucidated and their three-dimensional structures were recreated in silico using homology modelling and molecular dynamic simulation, which suggested that deep gas channels gradually developed in [NiFeSe] Hases under absolute anaerobic conditions, whereas the enzyme remained as a sealed edifice under environmental conditions of a higher oxygen exposure risk. The development of a gas cavity appears to be driven by non-synonymous mutations, which cause subtle conformational changes locally and distantly, even including highly conserved sequence regions.
authors.affiliation: Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan.|Institute of Industrial Science, the University of Tokyo, Komaba 153-8505, Japan.|PRESTO, Japan Science and Technology Agency, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Tamura
authors.affiliation: Institute of Industrial Science, the University of Tokyo, Komaba 153-8505, Japan.
authors.forename: Naoki
authors.initials: N
authors.lastname: Tsunekawa
authors.affiliation: Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan.
authors.forename: Michiko
authors.initials: M
authors.lastname: Nemoto
authors.affiliation: Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan.
authors.forename: Kenji
authors.initials: K
authors.lastname: Inagaki
authors.affiliation: Institute of Industrial Science, the University of Tokyo, Komaba 153-8505, Japan.
authors.forename: Toshiyuki
authors.initials: T
authors.lastname: Hirano
authors.affiliation: Institute of Industrial Science, the University of Tokyo, Komaba 153-8505, Japan.
authors.forename: Fumitoshi
authors.initials: F
authors.lastname: Sato
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D020134:Catalytic Domain; D003198:Computer Simulation; D019143:Evolution, Molecular; D006864:Hydrogenase / Q000737:chemistry* / Q000235:genetics; D020560:Proteobacteria / Q000201:enzymology* / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D006864:Hydrogenase
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