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TitleVisualizing the mechanism of quinol oxidation and inhibition of a -type oxidase using cryo-EM.
Journal, issue, pagesSci Adv, Vol. 12, Issue 21, Page eaec9946, Year 2026
Publish dateMay 22, 2026
AuthorsTijn T van der Velden / Kanwal Kayastha / Famke Pelser / Steffen Brünle / Lars J C Jeuken /
PubMed AbstractCytochrome 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 ...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.
External linksSci Adv / PubMed:42160434 / PubMed Central
MethodsEM (single particle)
Resolution2.23 - 2.61 Å
Structure data

54414

9rzv

EMDB-54414, PDB-9rzv:
E. coli cytochrome bd-I dimer bound to menaquinone
Method: EM (single particle) / Resolution: 2.23 Å

54801

9se4

EMDB-54801, PDB-9se4:
E. coli cytochrome bd-I monomer
Method: EM (single particle) / Resolution: 2.5 Å

54812

9sej

EMDB-54812, PDB-9sej:
E.coli cytochrome bd-I dimer bound to Aurachin D
Method: EM (single particle) / Resolution: 2.47 Å

54822

9sff

EMDB-54822, PDB-9sff:
E. coli cytochrome bd-I monomer
Method: EM (single particle) / Resolution: 2.38 Å

54823

9sfh

EMDB-54823, PDB-9sfh:
E.coli cytochrome bd-I monomer
Method: EM (single particle) / Resolution: 2.49 Å

54826

9sfj

EMDB-54826, PDB-9sfj:
E.coli cytochrome bd-I dimer in the MK bound open and closed state
Method: EM (single particle) / Resolution: 2.52 Å

54866

9sfv

EMDB-54866, PDB-9sfv:
E.coli cytochrome bd-I dimer in the apo and MK bound closed state
Method: EM (single particle) / Resolution: 2.61 Å

Chemicals

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

PDB-1jn4:
The Crystal Structure of Ribonuclease A in complex with 2'-deoxyuridine 3'-pyrophosphate (P'-5') adenosine

ChemComp-MQ9:
MENAQUINONE-9

ChemComp-LPP:
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / phospholipid*YM

ChemComp-UQ8:
Ubiquinone-8

ChemComp-OXY:
OXYGEN MOLECULE

ChemComp-PGT:
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / phospholipid*YM

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

ChemComp-HOH:
WATER

ChemComp-0NI:
Aurachin D

ChemComp-MQ8:
MENAQUINONE 8

Source
  • escherichia coli k-12 (bacteria)
  • Escherichia coli (E. coli)
KeywordsOXIDOREDUCTASE / Oxireductase / Complex / Quinone / Substrate / membrane protein / Escherichia coli / Respiration / Cytochrome

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