Molecular evolution of gas cavity in [NiFeSe] hydrogenases resurrected in silico

• Tamura, Takashi

• Tsunekawa, Naoki

• Nemoto, Michiko

• Inagaki, Kenji

• Hirano, Toshiyuki

• Sato, Fumitoshi

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.

Journal

• Scientific reports

  Scientific reports 6 19742-, 2016-01-28

  Nature Publishing Group

Keywords

• Multidisciplinary

Details

• CRID: 1050846637995650304
• NII Article ID: 120005723278
• ISSN: 20452322
• DOI: 10.1038/srep19742
• Web Site: https://ousar.lib.okayama-u.ac.jp/53953
• Web Site: https://www.nature.com/articles/srep19742
• Web Site: https://www.nature.com/articles/srep19742.pdf
• Text Lang: en
• Article Type: journal article
• Data Source:
  • IRDB
  • Crossref
  • CiNii Articles
  • KAKEN