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Structure paper

TitleMolecular interplay of an assembly machinery for nitrous oxide reductase.
Journal, issue, pagesNature, Vol. 608, Issue 7923, Page 626-631, Year 2022
Publish dateJul 27, 2022
AuthorsChristoph Müller / Lin Zhang / Sara Zipfel / Annika Topitsch / Marleen Lutz / Johannes Eckert / Benedikt Prasser / Mohamed Chami / Wei Lü / Juan Du / Oliver Einsle /
PubMed AbstractEmissions 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 ...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.
External linksNature / PubMed:35896743
MethodsEM (single particle)
Resolution3.04 - 4.5 Å
Structure data

EMDB-12683, PDB-7o0y:
ABC transporter NosDFY, nucleotide-free in GDN
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-12684, PDB-7o0z:
ABC transporter NosFY, nucleotide-free in GDN
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-12685, PDB-7o10:
ABC transporter NosDFY, nucleotide-free in GDN, R-domain 2
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-12686, PDB-7o11:
ABC transporter NosDFY, nucleotide-free in GDN, R-domain 1
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-12687, PDB-7o12:
ABC transporter NosDFY, AMPPNP-bound in GDN
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-12688, PDB-7o13:
ABC transporter NosDFY, nucleotide-free in lipid nanodisc
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-12689, PDB-7o14:
ABC transporter NosDFY, nucleotide-free in lipid nanodisc, R-domain 1
Method: EM (single particle)

EMDB-12690, PDB-7o15:
ABC transporter NosDFY, nucleotide-free in lipid nanodisc, R-domain 2
Method: EM (single particle)

EMDB-12691, PDB-7o16:
ABC transporter NosDFY, nucleotide-free in lipid nanodisc, R-domain 3
Method: EM (single particle)

EMDB-12692, PDB-7o17:
ABC transporter NosDFY E154Q, ATP-bound in lipid nanodisc
Method: EM (single particle) / Resolution: 4.5 Å

EMDB-13049, PDB-7osf:
ABC Transporter complex NosDFYL, R-domain 1
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-13050, PDB-7osg:
ABC Transporter complex NosDFYL, consensus refinement
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-13051, PDB-7osh:
ABC Transporter complex NosDFYL, R-domain 2
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-13052, PDB-7osi:
ABC Transporter complex NosDFYL, R-domain 3
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-13053, PDB-7osj:
ABC Transporter complex NosDFYL, membrane anchor
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-13885, PDB-7qba:
CryoEM structure of the ABC transporter NosDFY complexed with nitrous oxide reductase NosZ
Method: EM (single particle) / Resolution: 3.78 Å

EMDB-14813, PDB-7znq:
ABC transporter complex NosDFYL in GDN
Method: EM (single particle) / Resolution: 3.04 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-CU:
COPPER (II) ION

ChemComp-ZN:
Unknown entry

ChemComp-CA:
Unknown entry

Source
  • pseudomonas stutzeri atcc 14405 = ccug 16156 (bacteria)
  • pseudomonas stutzeri (bacteria)
KeywordsMEMBRANE PROTEIN / ABC Transporter complex / nucleotide-free / ABC Transporter / AMPPNP-bound / ATP-bound / metal-binding / ATP-free / metal binding protein / nitrous oxide reductase / ATP-binding-cassette transporter complex NosDFYL

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