Phosphorylation Mechanism of N-acetyl-L-Glutamate Kinase, a QM/MM Study

Inmicroorganisms and plants, NAGKN-acetyl-L-glutamate kinase (NAGK) catalyses the second step in L-argininesynthesis, the phosphorylation of N-Acetyl-L-glutamate(NAG) to give N-acetyl-L-glutamate-5-phosphate(NAGP). NAGK is only present in microorganisms and plants but absent frommammals, which makes it an attractive target for antimicrobial or biocidaldevelopment. Understanding the substrate binding mode and reaction mechanism ofNAGK is crucial for targeting the kinase to develop potential therapies. Here thesubstrate binding mode was studied by comparing the conformational change ofNAGK in the presence and in the absence of the NAG substrate based on moleculardynamic simulations. We revealed that with substrate binding the catalytic siteof the kinase involving three loops in NAGK exhibits a closed conformation,which is predominantly controlled by an interaction between Arg98 and the α-COO^-of NAG. Lys41 is found to guide phosphate transfer through the interactionswith the β-,γ-, and γ- phosphate oxygen atoms of ATP surrounded by two highlyconserved glycine residues (Gly44 and Gly76), while Arg98 helps to position theNAG substrate in the catalytic site, which facilitate the phosphate transfer. Furthermore,we elucidated phosphate transfer reaction mechanism using hybrid densityfunctional theory-based QM/MM calculations (B97D/AMBER99) and found that thecatalysis follows a dissociative mechanism.