7QBA

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular interplay of an assembly machinery for nitrous oxide reductase.

Muller, C.Zhang, L.Zipfel, S.Topitsch, A.Lutz, M.Eckert, J.Prasser, B.Chami, M.Lu, W.Du, J.Einsle, O.

(2022) Nature 

  • DOI: 10.1038/s41586-022-05015-2
  • Primary Citation of Related Structures:  
    7QBA, 7ZNQ

  • PubMed Abstract: 
  • Emissions of the critical ozone-depleting and greenhouse gas nitrous oxide (N 2 O) from soils and industrial processes have increased considerably over the last decades 1-3 . As the final step of bacterial denitrification, N 2 O is reduced to chemically inert N 2 (refs ...

    Emissions of the critical ozone-depleting and greenhouse gas nitrous oxide (N 2 O) from soils and industrial processes have increased considerably over the last decades 1-3 . As the final step of bacterial denitrification, N 2 O is reduced to chemically inert N 2 (refs. 1,4 ) in a reaction that is catalysed by the copper-dependent nitrous oxide reductase (N 2 OR) (ref. 5 ). The assembly of its unique [4Cu:2S] active site cluster Cu Z requires both the ATP-binding-cassette (ABC) complex NosDFY and the membrane-anchored copper chaperone NosL (refs. 4,6 ). Here we report cryo-electron microscopy structures of Pseudomonas stutzeri NosDFY and its complexes with NosL and N 2 OR, 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 N 2 OR requires a conformational change that is triggered by ATP binding. Mutually exclusive structures of NosDFY in complex with NosL and with N 2 OR 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 N 2 OR.


    Organizational Affiliation

    Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany. einsle@biochemie.uni-freiburg.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable ABC transporter binding protein NosDA436Pseudomonas stutzeriMutation(s): 0 
Gene Names: nosD
Membrane Entity: Yes 
UniProt
Find proteins for P19843 (Pseudomonas stutzeri)
Explore P19843 
Go to UniProtKB:  P19843
Entity Groups  
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UniProt GroupP19843
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Probable ABC transporter ATP-binding protein NosFB, C313Pseudomonas stutzeriMutation(s): 0 
Gene Names: nosF
Membrane Entity: Yes 
UniProt
Find proteins for P19844 (Pseudomonas stutzeri)
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Go to UniProtKB:  P19844
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UniProt GroupP19844
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Probable ABC transporter permease protein NosYD, E276Pseudomonas stutzeriMutation(s): 0 
Gene Names: nosY
Membrane Entity: Yes 
UniProt
Find proteins for P19845 (Pseudomonas stutzeri)
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Go to UniProtKB:  P19845
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UniProt GroupP19845
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrous-oxide reductaseF [auth H],
G [auth I]
646Pseudomonas stutzeriMutation(s): 0 
Gene Names: nosZ
EC: 1.7.2.4
Membrane Entity: Yes 
UniProt
Find proteins for P19573 (Pseudomonas stutzeri)
Explore P19573 
Go to UniProtKB:  P19573
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UniProt GroupP19573
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)Germany310656
German Research Foundation (DFG)GermanyCRC1381, 403222702
German Research Foundation (DFG)GermanyRTG2202, 46710898

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release
  • Version 1.1: 2022-08-10
    Changes: Database references