The Role of Arg228 in the phosphorylation of galactokinase: The mechanism of GHMP kinases by QM/MM studies

GHMP kinases are a group of structurally-related small molecule kinases. They have been found in all kingdoms of life and are mostly responsible for catalysing the ATP-dependent phosphorylation of intermediary metabolites. Although the GHMP kinases are of clinical, pharmaceutical and biotechnological importance, the mechanism of GHMP-kinases is controversial. A catalytic base mechanism was suggested for mevalonate kinase that has a structural feature of the ?-phosphate of ATP close to an aspartate residue; however, for one GHMP member, homoserine kinase, where the residue acting as general base is absent, a direct phosphorylation mechanism was suggested. Furthermore, it has been proposed by some authors that all the GHMP kinases function via the direct phosphorylation mechanism. This controversy in mechanism has limited our ability to exploit these enzymes as drug targets and in biotechnology. Here the phosphorylation reaction mechanism of the human galactokinase, a member of GHMP kinase was investigated using molecular dynamics simulations and density functional theory-based QM/MM calculations (B3LYP-D/AMBER99). The reaction coordinates were localized by potential energy scan using adiabatic mapping method. Our results indicate that a highly conserved Glu174 captures Arg105 to the proximity of the a-phosphate of ATP forming a H-bond network, therefore the mobility of ATP in the large oxyanion hole is restricted. Arg228 functions to stabilize the negative charge developed at the ß,?-bridging oxygen of the ATP during bond cleavage. The reaction occurs via direct phosphorylation mechanism and the Asp186 in proximity of ATP does not directly participate in the reaction pathway. Since Arg228 is not conserved among GHMP kinases, reagents which form interactions with Arg228, and therefore can interrupt its function in phosphorylation may be developed into potential selective inhibitors for galactokinase.