9R2G

Cytochrome bd II oxidase qOR-2 type from Mycobacterium smegmatis

Summary for 9R2G

• Entry DOI: 10.2210/pdb9r2g/pdb
• EMDB information: 53529
• Descriptor: Cytochrome bd menaquinol oxidase subunit I, Cytochrome bd-I oxidase subunit II, CARDIOLIPIN, ... (7 entities in total)
• Functional Keywords: membrane protein, actinobacteria, electron transport
• Biological source: Mycolicibacterium smegmatis (Mycobacterium smegmatis); More
• Total number of polymer chains: 2
• Total formula weight: 95183.19

Authors

Kovalova, T.,Janczak, M.,Adelroth, P.,Hogbom, M. (deposition date: 2025-04-30, release date: 2026-03-04, Last modification date: 2026-03-18)

Primary citation

Kovalova, T.,Janczak, M.,Gamiz-Hernandez, A.P.,Lundin, D.,Sharma, S.,Vilhjalmsdottir, J.,Sjostrand, D.,Kaila, V.R.I.,Hogbom, M.,Adelroth, P.
The Mycobacterium smegmatis bd -II terminal oxidase employs a carboxylate shift mechanism.
Proc.Natl.Acad.Sci.USA, 123:e2515348123-e2515348123, 2026

PubMed Abstract: Cytochrome is a terminal oxidase expressed under low oxygen conditions and central for the survival of many pathogens. Here, we characterize the cyt -II from , a member of a hitherto uncharacterized evolutionary group (qOR-2) of oxidases, by combining biochemical studies with cryo-electron microscopy (cryo-EM), and multiscale simulations. Overexpressing the operon in its native host led to production of a highly active -II ( = 30 e s) that together with a high-resolution (2.8 Å) cryo-EM structure and multiscale simulations reveal unique proton pathways and oxygen channels responsible for its function. We propose that a pH-dependent molecular switch, involving coordination changes of heme and surrounding bulky residues regulate substrate access into the active site. Taken together, our findings provide detailed mechanistic insight of qOR-2 type oxidases, and a basis for understanding the evolution of the superfamily.

PubMed: 41805574
DOI: 10.1073/pnas.2515348123

Experimental method

ELECTRON MICROSCOPY (2.8 Å)