7QBA

CryoEM structure of the ABC transporter NosDFY complexed with nitrous oxide reductase NosZ

Summary for 7QBA

• Entry DOI: 10.2210/pdb7qba/pdb
• EMDB information: 13885
• Descriptor: Probable ABC transporter binding protein NosD, Probable ABC transporter ATP-binding protein NosF, Probable ABC transporter permease protein NosY, ... (7 entities in total)
• Functional Keywords: abc transporter, metal binding protein, nitrous oxide reductase, membrane protein
• Biological source: Pseudomonas stutzeri (Pseudomonas perfectomarina); More
• Total number of polymer chains: 7
• Total formula weight: 321253.95

Authors

Zipfel, S.,Mueller, C.,Topitsch, A.,Lutz, M.,Zhang, L.,Einsle, O. (deposition date: 2021-11-18, release date: 2022-08-03, Last modification date: 2024-07-17)

Primary citation

Muller, C.,Zhang, L.,Zipfel, S.,Topitsch, A.,Lutz, M.,Eckert, J.,Prasser, B.,Chami, M.,Lu, W.,Du, J.,Einsle, O.
Molecular interplay of an assembly machinery for nitrous oxide reductase.
Nature, 608:626-631, 2022

PubMed Abstract: Emissions of the critical ozone-depleting and greenhouse gas nitrous oxide (NO) from soils and industrial processes have increased considerably over the last decades. As the final step of bacterial denitrification, NO is reduced to chemically inert N (refs. ) in a reaction that is catalysed by the copper-dependent nitrous oxide reductase (NOR) (ref. ). The assembly of its unique [4Cu:2S] active site cluster Cu requires both the ATP-binding-cassette (ABC) complex NosDFY and the membrane-anchored copper chaperone NosL (refs. ). Here we report cryo-electron microscopy structures of Pseudomonas stutzeri NosDFY and its complexes with NosL and NOR, respectively. We find that the periplasmic NosD protein contains a binding site for a Cu ion and interacts specifically with NosL in its nucleotide-free state, whereas its binding to NOR requires a conformational change that is triggered by ATP binding. Mutually exclusive structures of NosDFY in complex with NosL and with NOR reveal a sequential metal-trafficking and assembly pathway for a highly complex copper site. Within this pathway, NosDFY acts as a mechanical energy transducer rather than as a transporter. It links ATP hydrolysis in the cytoplasm to a conformational transition of the NosD subunit in the periplasm, which is required for NosDFY to switch its interaction partner so that copper ions are handed over from the chaperone NosL to the enzyme NOR.

PubMed: 35896743
DOI: 10.1038/s41586-022-05015-2

Experimental method

ELECTRON MICROSCOPY (3.78 Å)