Phosphorylation Mechanism of Phosphomevalonate Kinase: Implications for Rational Engineering of Isoprenoid Biosynthetic Pathway Enzymes

Mevalonate pathway is of important clinical, pharmaceutical and biotechnological relevance. However, lack of the understanding of the phosphorylation mechanism of the kinases in this pathway has limited rationally engineering the kinases in industry. Here the phosphorylation reaction mechanism of a representative kinase in the mevalonate pathway, phosphomevalonate kinase, was studied by using molecular dynamics and hybrid QM/MM methods. We find that a conserved residue (Ser106) is reorientated to anchor ATP via a stable H-bond interaction. In addition, Ser213 located on the α-helix at the catalytic site is repositioned to further approach the substrate, facilitating the proton transfer during the phosphorylation. Furthermore, we elucidate that Lys101 functions to neutralize the negative charge developed at the β-, γ-bridging oxygen atom of ATP during phosphoryl transfer. We demonstrate that the dissociative catalytic reaction occurs via a direct phosphorylation pathway. This is the first study on the phosphorylation mechanism of a mevalonate pathway kinase. The elucidation of the catalytic mechanism not only sheds light on the common catalytic mechanism of GHMP kinase superfamily, but also provides the structural basis for engineering the mevalonate pathway kinases to further exploit their applications in the production of a wide range of fine chemicals such as biofuels or pharmaceuticals. 

Understanding catalytic reactions over zeolites: A density functional theory study of selective catalytic reduction of NOX by NH3 over Cu-SAPO-34

Metal exchanged CHA-type (SAPO-34 and SSZ-13) zeolites are promising catalysts for selective catalytic reduction (SCR) of NOx by NH3. However, the understanding of the process at the molecular level is still limited, which hinders the identification of its mechanism and the design of more efficient zeolite catalysts. In this work, modelling the reaction over Cu-SAPO-34, a periodic density functional theory (DFT) study of NH3-SCR was performed using hybrid functional with the consideration of van der Waals (vdW) interactions. A mechanism with a low N–N coupling barrier is proposed to account for the activation of NO. The redox cycle of Cu2+ and Cu+, which is crucial for the SCR process, is identified with detailed analyses. Besides, the decomposition of NH2NO is shown to readily occur on the Brønsted acid site by a hydrogen push-pull mechanism, confirming the collective efforts of Brønsted acid and Lewis acid (Cu2+) sites. The special electronic and structural properties of Cu-SAPO-34 are demonstrated to play an essential role the reaction, which may have a general implication on the understanding of zeolite catalysis.