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	Cryo-EM captures the coordination of asymmetric electron transfer through a di-copper site in DPOR.
Journal, issue, pages	Nat Commun, Vol. 16, Issue 1, Page 3866, Year 2025
Publish date	Apr 24, 2025
Authors	Rajnandani Kashyap / Natalie Walsh / Jaigeeth Deveryshetty / Monika Tokmina-Lukaszewska / Kewei Zhao / Yunqiao J Gan / Brian M Hoffman / Ritimukta Sarangi / Brian Bothner / Brian Bennett / Edwin Antony /
PubMed Abstract	Enzymes that catalyze long-range electron transfer (ET) reactions often function as higher order complexes that possess two structurally symmetrical halves. The functional advantages for such an ...Enzymes that catalyze long-range electron transfer (ET) reactions often function as higher order complexes that possess two structurally symmetrical halves. The functional advantages for such an architecture remain a mystery. Using cryoelectron microscopy we capture snapshots of the nitrogenase-like dark-operative protochlorophyllide oxidoreductase (DPOR) during substrate binding and turnover. DPOR catalyzes reduction of the C17 = C18 double bond in protochlorophyllide during the dark chlorophyll biosynthetic pathway. DPOR is composed of electron donor (L-protein) and acceptor (NB-protein) component proteins that transiently form a complex in the presence of ATP to facilitate ET. NB-protein is an αβ heterotetramer with two structurally identical halves. However, our structures reveal that NB-protein becomes functionally asymmetric upon substrate binding. Asymmetry results in allosteric inhibition of L-protein engagement and ET in one half. Residues that form a conduit for ET are aligned in one half while misaligned in the other. An ATP hydrolysis-coupled conformational switch is triggered once ET is accomplished in one half. These structural changes are then relayed to the other half through a di-nuclear copper center at the tetrameric interface of the NB-protein and leads to activation of ET and substrate reduction. These findings provide a mechanistic blueprint for regulation of long-range electron transfer reactions.
External links	Nat Commun / PubMed:40274796 / PubMed Central
Methods	EM (single particle)
Resolution	2.7 - 3.82 Å
Structure data	43443 8vqh EMDB-43443, PDB-8vqh: CryoEM structure of BchN-BchB electron acceptor component protein of DPOR Method: EM (single particle) / Resolution: 2.7 Å 43444 8vqi EMDB-43444, PDB-8vqi: CryoEM structure of BchN-BchB electron acceptor component protein of DPOR with Pchlide Method: EM (single particle) / Resolution: 3.13 Å 43446 8vqj EMDB-43446, PDB-8vqj: CryoEM structure of DPOR under turnover Method: EM (single particle) / Resolution: 3.82 Å 44913 9buo EMDB-44913, PDB-9buo: CryoEM structure of DPOR in the presence of ADP-AlF3 Method: EM (single particle) / Resolution: 3.68 Å 47669 9e7h EMDB-47669, PDB-9e7h: CryoEM structure of BchN-BchB bound to Pchlide from the DPOR under turnover complex dataset Method: EM (single particle) / Resolution: 3.29 Å 47980 9efu EMDB-47980, PDB-9efu: CryoEM structure of BchN-BchB electron acceptor component protein of DPOR with Pchlide Method: EM (single particle) / Resolution: 2.92 Å
Chemicals	ChemComp-SF4: IRON/SULFUR CLUSTER ChemComp-CU: COPPER (II) ION ChemComp-HOH: WATER ChemComp-PMR: Protochlorophyllide ChemComp-MG: Unknown entry
Source	cereibacter sphaeroides (bacteria)
Keywords	OXIDOREDUCTASE / Plant Protein / Electron Transfer Enzymes / Photosynthesis