Phosphorylation Mechanism of Phosphomevalonate Kinase: Implications for Rational Engineering of Isoprenoid Biosynthetic Pathway Enzymes.
The 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 the 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.
School of Chemistry and Chemical Engineering, Queen's University Belfast , David Keir Building, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, United Kingdom.
Meilan
M
Huang
School of Chemistry and Chemical Engineering, Queen's University Belfast , David Keir Building, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, United Kingdom.
Kexin
K
Wei
School of Chemistry and Chemical Engineering, Queen's University Belfast , David Keir Building, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, United Kingdom.
Xiao
X
Li
School of Chemistry and Chemical Engineering, Queen's University Belfast , David Keir Building, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, United Kingdom.
James
J
McClory
School of Biotechnology and Chemical Engineering, Ningbo Institute of Technology, Zhejiang University , Ningbo 315100, China.
Guixiang
G
Hu
School of Biotechnology and Chemical Engineering, Ningbo Institute of Technology, Zhejiang University , Ningbo 315100, China.
Jian-Wei
JW
Zou
School of Pharmacy and Biomolecular Sciences, The University of Brighton , Huxley Building, Lewes Road, Brighton, BN2 4GJ, United Kingdom.
David
D
Timson