9SE4

E. coli cytochrome bd-I monomer

This is a non-PDB format compatible entry.

Summary for 9SE4

• Entry DOI: 10.2210/pdb9se4/pdb
• Related: 9rzv
• EMDB information: 54801
• Descriptor: Cytochrome bd-I ubiquinol oxidase subunit 1, Cytochrome bd-I ubiquinol oxidase subunit 2, Cytochrome bd-I ubiquinol oxidase CydH (Uncharacterized protein YnhF), ... (10 entities in total)
• Functional Keywords: respiration, complex, cytochrome, oxidoreductase
• Biological source: Escherichia coli K-12; More
• Total number of polymer chains: 4
• Total formula weight: 111701.25

Authors

van der Velden, T.T.,Kayastha, K.,Bruenle, S.,Jeuken, L.J.C. (deposition date: 2025-08-15, release date: 2026-04-22, Last modification date: 2026-06-10)

Primary citation

van der Velden, T.T.,Kayastha, K.,Pelser, F.,Brunle, S.,Jeuken, L.J.C.
Visualizing the mechanism of quinol oxidation and inhibition of a bd -type oxidase using cryo-EM.
Sci Adv, 12:eaec9946-eaec9946, 2026

PubMed Abstract: Cytochrome is a prokaryotic terminal oxidase recognized as an antibiotic target against various pathogens. Despite its critical role in respiration, failure to capture the mechanism of quinol oxidation and inhibition prohibits structure guided drug discovery. Here, we present cryo-electron microscopy structures of cytochrome -I in monomeric and dimeric forms, in several quinone and inhibitor-bound states. We identify a dynamic Q-loop lid that undergoes a disorder-to-order transition upon substrate binding to the dimer, completing the active site and enabling catalysis. Structure-guided mutagenesis confirms Tyr243 and Arg298 as conserved catalytic residues only found in long Q-loop oxidases, highlighting evolutionary divergence from other subfamilies. Inhibition by Aurachin D triggers refolding of the active site, occluding substrate access via an Asp239-mediated mechanism. The structural and mechanistic insights presented here establish a comprehensive framework, opening paths for drug discovery against oxidases.

PubMed: 42160434
DOI: 10.1126/sciadv.aec9946

Experimental method

ELECTRON MICROSCOPY (2.5 Å)