Cluster Model Study into the Catalytic Mechanism of ?-Ketoglutarate Biodegradation by the Ethylene-Forming Enzyme Reveals Structural Differences with Nonheme Iron Hydroxylases

Ethylene is an important signaling molecule in plants that triggers the growth of leaves, flowers, and fruits. One enzymes involved biosynthesis ethylene ethylene-forming enzyme (EFE), which usual nonheme iron biodegrades ?-ketoglutarate into three CO2 molecules ethylene. As detailed mechanism EFE remains controversial particularly function co-substrate l-arginine, we decided to pursue a density functional theory study on possible pathways leading test many mechanisms. A large active site cluster model 322 atoms was created, contains all features first- second-coordination sphere substrate (?-ketoglutarate) binding pockets. The calculations identify persuccinate intermediate bifurcation pathway either react with form carbonate or forms high-valent iron(IV)-oxo species through heterolytic dioxygen bond cleavage. Our studies show both converge same again can lead products, although two have different kinetics. Interestingly, our also itself but much higher barriers. matter fact, these barriers are energy than typical aliphatic hydroxylation may not be competitive arginine hydroxylation. Inclusion l-arginine leads minor changes structure fold, its charge dipole moment does seem affect first stage catalytic cycle. Moreover, key activation less affected by inclusion model. We, therefore, believe role lock products tight pocket enable degradation prevent early release CO2. due distinct differences positioning between activating dioxygenases tighter EFE, predict prevented oxygen mechanism. This enables attack complex formation. work gives suggestions engineering hydroxylase improving biosynthesis.