3USC

Crystal Structure of E. coli hydrogenase-1 in a ferricyanide-oxidized form

3USC の概要

• エントリーDOI: 10.2210/pdb3usc/pdb
• 関連するPDBエントリー: 3UQY 3USE
• 分子名称: Hydrogenase-1 small chain, NICKEL (III) ION, MAGNESIUM ION, ... (13 entities in total)
• 機能のキーワード: membrane-bound hydrogenase, oxidoreductase
• 由来する生物種: Escherichia coli; 詳細
• 細胞内の位置: Cell inner membrane; Single-pass type I membrane protein; Periplasmic side: P69739; Cell membrane; Peripheral membrane protein: P0ACD8
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 207093.61

構造登録者

Volbeda, A.,Fontecilla-Camps, J.C.,Darnault, C. (登録日: 2011-11-23, 公開日: 2012-03-28, 最終更新日: 2024-04-03)

主引用文献

Volbeda, A.,Amara, P.,Darnault, C.,Mouesca, J.M.,Parkin, A.,Roessler, M.M.,Armstrong, F.A.,Fontecilla-Camps, J.C.
X-ray crystallographic and computational studies of the O2-tolerant [NiFe]-hydrogenase 1 from Escherichia coli.
Proc.Natl.Acad.Sci.USA, 109:5305-5310, 2012

PubMed Abstract: The crystal structure of the membrane-bound O(2)-tolerant [NiFe]-hydrogenase 1 from Escherichia coli (EcHyd-1) has been solved in three different states: as-isolated, H(2)-reduced, and chemically oxidized. As very recently reported for similar enzymes from Ralstonia eutropha and Hydrogenovibrio marinus, two supernumerary Cys residues coordinate the proximal [FeS] cluster in EcHyd-1, which lacks one of the inorganic sulfide ligands. We find that the as-isolated, aerobically purified species contains a mixture of at least two conformations for one of the cluster iron ions and Glu76. In one of them, Glu76 and the iron occupy positions that are similar to those found in O(2)-sensitive [NiFe]-hydrogenases. In the other conformation, this iron binds, besides three sulfur ligands, the amide N from Cys20 and one Oε of Glu76. Our calculations show that oxidation of this unique iron generates the high-potential form of the proximal cluster. The structural rearrangement caused by oxidation is confirmed by our H(2)-reduced and oxidized EcHyd-1 structures. Thus, thanks to the peculiar coordination of the unique iron, the proximal cluster can contribute two successive electrons to secure complete reduction of O(2) to H(2)O at the active site. The two observed conformations of Glu76 are consistent with this residue playing the role of a base to deprotonate the amide moiety of Cys20 upon iron binding and transfer the resulting proton away, thus allowing the second oxidation to be electroneutral. The comparison of our structures also shows the existence of a dynamic chain of water molecules, resulting from O(2) reduction, located near the active site.

PubMed: 22431599
DOI: 10.1073/pnas.1119806109

実験手法

X-RAY DIFFRACTION (2 Å)