Structure of Escherichia coli cytochrome bd-II type oxidase with bound aurachin D

Antonia Grauel,Stefan Günther,Aurélien F A Moumbock,Thorsten Friedrich,Frederic Melin,Jan Kägi,Sabrina Oppermann,Rolf Müller,Petra Hellwig,Iryna Makarchuk,Tim Rasmussen,Bettina Böttcher,Daniel Wohlwend

doi:10.1038/s41467-021-26835-2

Abstract

Cytochrome bd quinol:O2 oxidoreductases are respiratory terminal oxidases so far only identified in prokaryotes, including several pathogenic bacteria. Escherichia coli contains two bd oxidases of which only the bd-I type is structurally characterized. Here, we report the structure of the Escherichia coli cytochrome bd-II type oxidase with the bound inhibitor aurachin D as obtained by electron cryo-microscopy at 3 Å resolution. The oxidase consists of subunits AppB, C and X that show an architecture similar to that of bd-I. The three heme cofactors are found in AppC, while AppB is stabilized by a structural ubiquinone-8 at the homologous positions. A fourth subunit present in bd-I is lacking in bd-II. Accordingly, heme b595 is exposed to the membrane but heme d embedded within the protein and showing an unexpectedly high redox potential is the catalytically active centre. The structure of the Q-loop is fully resolved, revealing the specific aurachin binding.

Highlights

Cytochrome bd quinol:O2 oxidoreductases are respiratory terminal oxidases so far only identified in prokaryotes, including several pathogenic bacteria
Membrane proteins were extracted with the detergent lauryl maltose neopentyl glycol (LMNG) and purified by affinity- and size exclusionchromatography (Supplementary Fig. 1)
The major bands of the gel were identified as AppC and AppB by mass spectrometry (AppC: sequence coverage: 33%, overall score 69; AppB: sequence coverage: 3%, overall score 19)

Summary

Introduction

Cytochrome bd quinol:O2 oxidoreductases are respiratory terminal oxidases so far only identified in prokaryotes, including several pathogenic bacteria. Escherichia coli contains two bd oxidases of which only the bd-I type is structurally characterized. 1234567890():,; Cytochrome bd quinol:dioxygen oxidases (called bd oxidases for simplicity hereafter) are terminal reductases exclusively found in bacterial and archaeal respiratory chains. Bd oxidases contribute to the generation of a protonmotive force (pmf) by a vectorial charge transfer[4,5] They display a high affinity towards dioxygen, enabling growth under microaerobic conditions and endow pathogens such as Shigella flexneri[6], Mycobacterium tuberculosis[7], and various streptococcus species[8] with resistance to intracellular stressors such as NO and intracellular hypoxia, making them excellent drug targets. CydA by a pseudo twofold symmetry and contains a structural ubiquinone-8 at a position occupied by the hemes in CydA21,22

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Results

Conclusion