7CUB

2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane

7CUB の概要

• エントリーDOI: 10.2210/pdb7cub/pdb
• EMDBエントリー: 30471
• 分子名称: Cytochrome bo(3) ubiquinol oxidase subunit 1, Cytochrome bo(3) ubiquinol oxidase subunit 2, Cytochrome bo(3) ubiquinol oxidase subunit 3, ... (10 entities in total)
• 機能のキーワード: proton pump, ubiquinol, oxidase, oxidoreductase
• 由来する生物種: Escherichia coli; 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 147340.73

構造登録者

Li, J.,Han, L.,Gennis, R.B.,Zhu, J.P.,Zhang, K. (登録日: 2020-08-22, 公開日: 2021-08-25, 最終更新日: 2024-05-29)

主引用文献

Li, J.,Han, L.,Vallese, F.,Ding, Z.,Choi, S.K.,Hong, S.,Luo, Y.,Liu, B.,Chan, C.K.,Tajkhorshid, E.,Zhu, J.,Clarke, O.,Zhang, K.,Gennis, R.
Cryo-EM structures of Escherichia coli cytochrome bo3 reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site.
Proc.Natl.Acad.Sci.USA, 118:-, 2021

PubMed Abstract: Two independent structures of the proton-pumping, respiratory cytochrome ubiquinol oxidase (cyt ) have been determined by cryogenic electron microscopy (cryo-EM) in styrene-maleic acid (SMA) copolymer nanodiscs and in membrane scaffold protein (MSP) nanodiscs to 2.55- and 2.19-Å resolution, respectively. The structures include the metal redox centers (heme , heme , and Cu), the redox-active cross-linked histidine-tyrosine cofactor, and the internal water molecules in the proton-conducting D channel. Each structure also contains one equivalent of ubiquinone-8 (UQ8) in the substrate binding site as well as several phospholipid molecules. The isoprene side chain of UQ8 is clamped within a hydrophobic groove in subunit I by transmembrane helix TM0, which is only present in quinol oxidases and not in the closely related cytochrome oxidases. Both structures show carbonyl O1 of the UQ8 headgroup hydrogen bonded to D75 and R71 In both structures, residue H98 occupies two conformations. In conformation 1, H98 forms a hydrogen bond with carbonyl O4 of the UQ8 headgroup, but in conformation 2, the imidazole side chain of H98 has flipped to form a hydrogen bond with E14 at the N-terminal end of TM0. We propose that H98 dynamics facilitate proton transfer from ubiquinol to the periplasmic aqueous phase during oxidation of the substrate. Computational studies show that TM0 creates a channel, allowing access of water to the ubiquinol headgroup and to H98.

PubMed: 34417297
DOI: 10.1073/pnas.2106750118

実験手法

ELECTRON MICROSCOPY (2.55 Å)