9V6B

Neutron crystal structure of the oxidized form of b5R at pD 6.5

Summary for 9V6B

• Entry DOI: 10.2210/pdb9v6b/pdb
• Descriptor: NADH-cytochrome b5 reductase 3, FLAVIN-ADENINE DINUCLEOTIDE, GLYCEROL, ... (4 entities in total)
• Functional Keywords: fatty acid synthesis, methemoglobin reduction, xenobiotic oxidation, antioxidant defense, oxidoreductase
• Biological source: Sus scrofa (pig)
• Total number of polymer chains: 1
• Total formula weight: 32118.71

Authors

Hirano, Y.,Kurihara, K.,Kusaka, K.,Ostermann, A.,Hikita, M.,Kimura, S.,Miki, K.,Tamada, T. (deposition date: 2025-05-27, release date: 2025-11-19)

Primary citation

Hirano, Y.,Kurihara, K.,Kusaka, K.,Ostermann, A.,Hikita, M.,Kimura, S.,Miki, K.,Tamada, T.
Structural basis of hydride and proton transfer reactions revealed by the detection of hydrogen atoms in mammalian NADH-cytochrome b 5 reductase.
Structure, 2025

PubMed Abstract: Many structural studies have been reported for ferredoxin:NADP reductase family members, but an experimental validation of the catalytic hydride and proton transfer steps through a direct detection of the involved hydrogen atoms has not been achieved so far. Here, we determined high-resolution X-ray and neutron crystal structures of NADH-cytochrome b reductase, which acts as an electron supplier for various metabolic processes and mediates hydride and proton transfer reactions via its FAD and NADH cofactors. The X-ray structures identify the FADH-NAD and FAD-NADH complexes based on the electron densities of the hydrogen atoms bound to the cofactors. The neutron structures determined at different pD-values show a difference in the protonation state of the histidine residue in the hydrogen-bond network from FAD to the protein surface. The observation of the hydrogen atoms reveals the structural basis for the hydride and proton transfer reactions catalyzed by NADH-cytochrome b reductase.

PubMed: 41172987
DOI: 10.1016/j.str.2025.10.006

Experimental method

NEUTRON DIFFRACTION (1.6 Å)