Coordination dynamics of iron center enables the C–H bond activation: QM/MM insight into the catalysis of hydroxyglutarate synthase (HglS)

Hydroxyglutarate synthase (HglS) from Pseudomonas putida is an iron (II) dependent non-heme oxygenase, which is responsible for the biodegradation of 2-oxoadipate (2OA) to D-2-hydroxyglutarate (D-2HG) in plant lysine catabolism. Here detailed mechanisms for the chemical steps involved in decarboxylation and hydroxylation in the biodegradation of 2OA have been explored by extensive MD simulations and QM/MM calculations. Our study revealed the existence of two coordination modes of the Fe(IV)-oxo species during the reactions of HglS, and the "proximal" one is responsible for the C–H bond activation. The reaction initiates with the attack of Fe(III)-superoxo species on 2OA, resulting in the FeII-O-O-2OA species. After the release of CO2 and the subsequent O-O cleavage, the reactions lead to the "distal" Fe(IV)-oxo species. This species can undergo a coordination switch to evolve into the "proximal" conformation of Fe(IV)-oxo, which is the rate-limiting step with an energy barrier of 20.6 kcal/mol. Moreover, residues in the second coordination sphere, including Arg74, Gln266, Val402, and Ser403, not only strengthen the substrate binding but also facilitate the ferryl-flip, leading to the "proximal" Fe(IV)-oxo conformation that is ideal for the C–H bond activation. These findings may expand our understanding of the coordination dynamics of the iron center in HglS enzyme, which has general implications for other non-heme oxygenases.