Cryo-EM structure of mycobacterial cytochrome bd reveals two oxygen access channels

Weiwei Wang, Yan Gao, Yanting Tang, Xiaoting Zhou, Yuezheng Lai, Shan Zhou, Yuying Zhang, Xiuna Yang, Fengjiang Liu, Luke W. Guddat, Quan Wang (), Zihe Rao () and Hongri Gong ()
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Weiwei Wang: ShanghaiTech University
Yan Gao: ShanghaiTech University
Yanting Tang: Nankai University
Xiaoting Zhou: ShanghaiTech University
Yuezheng Lai: Nankai University
Shan Zhou: Nankai University
Yuying Zhang: Nankai University
Xiuna Yang: ShanghaiTech University
Fengjiang Liu: ShanghaiTech University
Luke W. Guddat: The University of Queensland
Quan Wang: ShanghaiTech University
Zihe Rao: ShanghaiTech University
Hongri Gong: Nankai University

Nature Communications, 2021, vol. 12, issue 1, 1-8

Abstract: Abstract Cytochromes bd are ubiquitous amongst prokaryotes including many human-pathogenic bacteria. Such complexes are targets for the development of antimicrobial drugs. However, an understanding of the relationship between the structure and functional mechanisms of these oxidases is incomplete. Here, we have determined the 2.8 Å structure of Mycobacterium smegmatis cytochrome bd by single-particle cryo-electron microscopy. This bd oxidase consists of two subunits CydA and CydB, that adopt a pseudo two-fold symmetrical arrangement. The structural topology of its Q-loop domain, whose function is to bind the substrate, quinol, is significantly different compared to the C-terminal region reported for cytochromes bd from Geobacillus thermodenitrificans (G. th) and Escherichia coli (E. coli). In addition, we have identified two potential oxygen access channels in the structure and shown that similar tunnels also exist in G. th and E. coli cytochromes bd. This study provides insights to develop a framework for the rational design of antituberculosis compounds that block the oxygen access channels of this oxidase.

Date: 2021
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DOI: 10.1038/s41467-021-24924-w

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