9BUO
CryoEM structure of DPOR in the presence of ADP-AlF3
Summary for 9BUO
| Entry DOI | 10.2210/pdb9buo/pdb |
| EMDB information | 44913 |
| Descriptor | Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein, Light-independent protochlorophyllide reductase subunit N, Light-independent protochlorophyllide reductase subunit B, ... (6 entities in total) |
| Functional Keywords | plant protein, electron transfer enzymes, photosynthesis, oxidoreductase |
| Biological source | Cereibacter sphaeroides More |
| Total number of polymer chains | 8 |
| Total formula weight | 351142.94 |
| Authors | |
| Primary citation | Kashyap, R.,Walsh, N.,Deveryshetty, J.,Tokmina-Lukaszewska, M.,Zhao, K.,Gan, Y.J.,Hoffman, B.M.,Sarangi, R.,Bothner, B.,Bennett, B.,Antony, E. Cryo-EM captures the coordination of asymmetric electron transfer through a di-copper site in DPOR. Nat Commun, 16:3866-3866, 2025 Cited by 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 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. PubMed: 40274796DOI: 10.1038/s41467-025-59158-7 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.68 Å) |
Structure validation
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