Cryo-EM structure of cytochrome bo3 quinol oxidase assembled in peptidiscs reveals an "open" conformation for potential ubiquinone-8 release

Ye Gao; Yue Zhang; Sneha Hakke; Ronny Mohren; Lyanne J P M Sijbers; Peter J Peters; Raimond B G Ravelli

doi:10.1016/j.bbabio.2024.149045

Cryo-EM structure of cytochrome bo₃ quinol oxidase assembled in peptidiscs reveals an "open" conformation for potential ubiquinone-8 release

Biochim Biophys Acta Bioenerg. 2024 Apr 11;1865(3):149045. doi: 10.1016/j.bbabio.2024.149045. Online ahead of print.

Authors

Ye Gao¹, Yue Zhang², Sneha Hakke², Ronny Mohren², Lyanne J P M Sijbers², Peter J Peters³, Raimond B G Ravelli²

Affiliations

¹ Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands; Division of Imaging Mass Spectrometry, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands. Electronic address: y.gao@maastrichtuniversity.nl.
² Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands; Division of Imaging Mass Spectrometry, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands.
³ Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands; Division of Imaging Mass Spectrometry, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands. Electronic address: pj.peters@maastrichtuniversity.nl.

PMID: 38614453
DOI: 10.1016/j.bbabio.2024.149045

Abstract

Cytochrome bo₃ quinol oxidase belongs to the heme‑copper-oxidoreductase (HCO) superfamily, which is part of the respiratory chain and essential for cell survival. While the reaction mechanism of cyt bo₃ has been studied extensively over the last decades, specific details about its substrate binding and product release have remained unelucidated due to the lack of structural information. Here, we report a 2.8 Å cryo-electron microscopy structure of cyt bo₃ from Escherichia coli assembled in peptidiscs. Our structural model shows a conformation for amino acids 1-41 of subunit I different from all previously published structures while the remaining parts of this enzyme are similar. Our new conformation shows a "U-shape" assembly in contrast to the transmembrane helix, named "TM0", in other reported structural models. However, TM0 blocks ubiquinone-8 (reaction product) release, suggesting that other cyt bo₃ conformations should exist. Our structural model presents experimental evidence for an "open" conformation to facilitate substrate/product exchange. This work helps further understand the reaction cycle of this oxidase, which could be a benefit for potential drug/antibiotic design for health science.

Keywords: Cytochrome oxidase; Escherichia coli (E. coli); Ni-NTA resin; Peptidisc; Single particle analysis; Ubiquinone.