7D5I

Structure of Mycobacterium smegmatis bd complex in the apo-form.

Summary for 7D5I

• Entry DOI: 10.2210/pdb7d5i/pdb
• EMDB information: 30582
• Descriptor: Cytochrome D ubiquinol oxidase subunit 1, Integral membrane cytochrome D ubiquinol oxidase (Subunit II) CydB, HEME B/C, ... (4 entities in total)
• Functional Keywords: mycobacterium smegmatis, electron transfer chain, oxidoreductase
• Biological source: Mycolicibacterium smegmatis MC2 155; More
• Total number of polymer chains: 2
• Total formula weight: 95220.11

Authors

Wang, W.,Gong, H.,Gao, Y.,Zhou, X.,Rao, Z. (deposition date: 2020-09-26, release date: 2021-06-23, Last modification date: 2025-07-02)

Primary citation

Wang, W.,Gao, Y.,Tang, Y.,Zhou, X.,Lai, Y.,Zhou, S.,Zhang, Y.,Yang, X.,Liu, F.,Guddat, L.W.,Wang, Q.,Rao, Z.,Gong, H.
Cryo-EM structure of mycobacterial cytochrome bd reveals two oxygen access channels.
Nat Commun, 12:4621-4621, 2021

PubMed 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.

PubMed: 34330928
DOI: 10.1038/s41467-021-24924-w

Experimental method

ELECTRON MICROSCOPY (2.79 Å)