7OSI

ABC Transporter complex NosDFYL, R-domain 3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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 608: 626-631

  • DOI: https://doi.org/10.1038/s41586-022-05015-2

  • 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. 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ABC transporter binding protein NosD436Stutzerimonas stutzeri ATCC 14405 = CCUG 16156Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P19843 (Stutzerimonas stutzeri)
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Go to UniProtKB:  P19843
Entity Groups  
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UniProt GroupP19843
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ABC transporter ATP-binding protein NosF
B, C
308Stutzerimonas stutzeri ATCC 14405 = CCUG 16156Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P19844 (Stutzerimonas stutzeri)
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Go to UniProtKB:  P19844
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UniProt GroupP19844
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ABC transporter permease protein NosY
D, E
276Stutzerimonas stutzeri ATCC 14405 = CCUG 16156Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P19845 (Stutzerimonas stutzeri)
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Go to UniProtKB:  P19845
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UniProt GroupP19845
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Copper-binding lipoprotein NosLF [auth H]190Stutzerimonas stutzeri ATCC 14405 = CCUG 16156Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q52529 (Stutzerimonas stutzeri)
Explore Q52529 
Go to UniProtKB:  Q52529
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UniProt GroupQ52529
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references