Homologous bd oxidases share the same architecture but differ in mechanism

Nat Commun. 2019 Nov 13;10(1):5138. doi: 10.1038/s41467-019-13122-4.

Abstract

Cytochrome bd oxidases are terminal reductases of bacterial and archaeal respiratory chains. The enzyme couples the oxidation of ubiquinol or menaquinol with the reduction of dioxygen to water, thus contributing to the generation of the protonmotive force. Here, we determine the structure of the Escherichia coli bd oxidase treated with the specific inhibitor aurachin by cryo-electron microscopy (cryo-EM). The major subunits CydA and CydB are related by a pseudo two fold symmetry. The heme b and d cofactors are found in CydA, while ubiquinone-8 is bound at the homologous positions in CydB to stabilize its structure. The architecture of the E. coli enzyme is highly similar to that of Geobacillus thermodenitrificans, however, the positions of heme b595 and d are interchanged, and a common oxygen channel is blocked by a fourth subunit and substituted by a more narrow, alternative channel. Thus, with the same overall fold, the homologous enzymes exhibit a different mechanism.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cytochrome b Group / chemistry*
  • Cytochrome b Group / metabolism*
  • Cytochrome b Group / ultrastructure
  • Electron Transport Chain Complex Proteins / chemistry*
  • Electron Transport Chain Complex Proteins / metabolism*
  • Electron Transport Chain Complex Proteins / ultrastructure
  • Escherichia coli / enzymology*
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / metabolism*
  • Escherichia coli Proteins / ultrastructure
  • Geobacillus / enzymology
  • Heme / chemistry
  • Heme / metabolism
  • Models, Molecular
  • Oxidoreductases / chemistry*
  • Oxidoreductases / metabolism*
  • Oxidoreductases / ultrastructure
  • Oxygen / metabolism
  • Protons
  • Sequence Homology, Amino Acid*
  • Substrate Specificity
  • Ubiquinone / chemistry
  • Ubiquinone / metabolism
  • Water

Substances

  • Cytochrome b Group
  • Electron Transport Chain Complex Proteins
  • Escherichia coli Proteins
  • Protons
  • Water
  • Ubiquinone
  • Heme
  • ubiquinone 8
  • Oxidoreductases
  • cytochrome bd terminal oxidase complex, E coli
  • Oxygen