7ZNQ

ABC transporter complex NosDFYL in GDN


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 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: 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 ATP-binding protein NosFB [auth F],
A [auth f]
308Pseudomonas stutzeri ATCC 14405 = CCUG 16156Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P19844 (Pseudomonas stutzeri)
Explore P19844 
Go to UniProtKB:  P19844
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19844
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Probable ABC transporter permease protein NosYC [auth Y],
D [auth y]
276Pseudomonas stutzeri ATCC 14405 = CCUG 16156Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P19845 (Pseudomonas stutzeri)
Explore P19845 
Go to UniProtKB:  P19845
Entity Groups  
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UniProt GroupP19845
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Probable ABC transporter binding protein NosDE [auth D]436Pseudomonas stutzeri ATCC 14405 = CCUG 16156Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P19843 (Pseudomonas stutzeri)
Explore P19843 
Go to UniProtKB:  P19843
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UniProt GroupP19843
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Copper-binding lipoprotein NosLF [auth L]198Pseudomonas stutzeri ATCC 14405 = CCUG 16156Mutation(s): 0 
Gene Names: nosL
Membrane Entity: Yes 
UniProt
Find proteins for Q52529 (Pseudomonas stutzeri)
Explore Q52529 
Go to UniProtKB:  Q52529
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UniProt GroupQ52529
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
I [auth L]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CU (Subject of Investigation/LOI)
Query on CU

Download Ideal Coordinates CCD File 
H [auth D]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 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)European Union310656
German Research Foundation (DFG)Germany403222702
German Research Foundation (DFG)Germany192904750

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
  • Version 1.2: 2022-08-31
    Changes: Database references