Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Molecular interplay of an assembly machinery for nitrous oxide reductase.
Journal, issue, pages	Nature, Vol. 608, Issue 7923, Page 626-631, Year 2022
Publish date	Jul 27, 2022
Authors	Christoph Müller / Lin Zhang / Sara Zipfel / Annika Topitsch / Marleen Lutz / Johannes Eckert / Benedikt Prasser / Mohamed Chami / Wei Lü / Juan Du / Oliver Einsle /
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 ...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 links	Nature / PubMed:35896743
Methods	EM (single particle)
Resolution	3.04 - 4.5 Å
Structure data	12683 7o0y EMDB-12683, PDB-7o0y: ABC transporter NosDFY, nucleotide-free in GDN Method: EM (single particle) / Resolution: 3.3 Å 12684 7o0z EMDB-12684, PDB-7o0z: ABC transporter NosFY, nucleotide-free in GDN Method: EM (single particle) / Resolution: 3.7 Å 12685 7o10 EMDB-12685, PDB-7o10: ABC transporter NosDFY, nucleotide-free in GDN, R-domain 2 Method: EM (single particle) / Resolution: 3.6 Å 12686 7o11 EMDB-12686, PDB-7o11: ABC transporter NosDFY, nucleotide-free in GDN, R-domain 1 Method: EM (single particle) / Resolution: 3.7 Å 12687 7o12 EMDB-12687, PDB-7o12: ABC transporter NosDFY, AMPPNP-bound in GDN Method: EM (single particle) / Resolution: 3.7 Å 12688 7o13 EMDB-12688, PDB-7o13: ABC transporter NosDFY, nucleotide-free in lipid nanodisc Method: EM (single particle) / Resolution: 3.6 Å 12689 7o14 EMDB-12689, PDB-7o14: ABC transporter NosDFY, nucleotide-free in lipid nanodisc, R-domain 1 Method: EM (single particle) 12690 7o15 EMDB-12690, PDB-7o15: ABC transporter NosDFY, nucleotide-free in lipid nanodisc, R-domain 2 Method: EM (single particle) 12691 7o16 EMDB-12691, PDB-7o16: ABC transporter NosDFY, nucleotide-free in lipid nanodisc, R-domain 3 Method: EM (single particle) 12692 7o17 EMDB-12692, PDB-7o17: ABC transporter NosDFY E154Q, ATP-bound in lipid nanodisc Method: EM (single particle) / Resolution: 4.5 Å 13049 7osf EMDB-13049, PDB-7osf: ABC Transporter complex NosDFYL, R-domain 1 Method: EM (single particle) / Resolution: 3.8 Å 13050 7osg EMDB-13050, PDB-7osg: ABC Transporter complex NosDFYL, consensus refinement Method: EM (single particle) / Resolution: 3.3 Å 13051 7osh EMDB-13051, PDB-7osh: ABC Transporter complex NosDFYL, R-domain 2 Method: EM (single particle) / Resolution: 3.8 Å 13052 7osi EMDB-13052, PDB-7osi: ABC Transporter complex NosDFYL, R-domain 3 Method: EM (single particle) / Resolution: 3.8 Å 13053 7osj EMDB-13053, PDB-7osj: ABC Transporter complex NosDFYL, membrane anchor Method: EM (single particle) / Resolution: 3.8 Å 13885 7qba 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 14813 7znq 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 / Water ChemComp-ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogueYM ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM / Adenosine triphosphate ChemComp-CU: COPPER (II) ION / Copper ChemComp-ZN: Unknown entry ChemComp-CA: Unknown entry
Source	pseudomonas stutzeri atcc 14405 = ccug 16156 (bacteria) pseudomonas stutzeri (bacteria)
Keywords	MEMBRANE 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