Nucleoside diphosphate kinase mechanism

Schneider, B. Babolat, M. Xu, Y.W. Janin, J. Veron, M. Deville-Bonne, D. Mechanism of phosphoryl transfer by nucleoside diphosphate kinase pH dependence and role of the active site Lysl6 and Tyr56 residues. Eur. J. Biochem., 268, 1964-1971 (2001)... 

Gonin, P. Xu, Y Milon, L. Dabernat, S. Morr, M. Kumar, R. Lacombe, M.L. Janin, J. Lascu, I. Catalytic mechanism of nucleoside diphosphate kinase investigated using nucleotide analogues, viscosity effects, and X-ray crystallography. Biochemistry, 38, 7265-7272 (1999)... 

FIGURE 13-12 Ping-Pong mechanism of nucleoside diphosphate kinase. The enzyme binds its first substrate (ATP in our example), and a phosphoryl group is transferred to the side chain of a His residue. ADP departs, and another nucleoside (or deoxynucleoside) diphos-... 

The deoxycytidine phosphates result from reduction of CDP to dCDP by a mechanism analogous to that described for the purine nucleotides. Then dCDP is converted to dCTP by nucleoside diphosphate kinase. 

Again, the configuration is inverted. Nucleoside diphosphate kinase catalyzes the same transfer, but to a nucleoside diphosphate rather than to AMP, and with retention of configuration rather than with inversion (70). The mechanism of action of adenylate kinase involves a single displacement at P and that of nucleoside diphosphate kinase involves a double displacement at P via an intermediate phosphoenzyme. Although alkaline phosphatase is not classified as a phosphotransferase, it catalyzes transphosphorylation via the same phosphoenzyme that is the intermediate in the phosphatase reaction. This enzyme catalyzes reaction... 

In some kinases, such as nucleoside diphosphate kinase, " an intermediate step is the phosphoryl transfer to a group belonging to the enzyme, as happens in ATPase and as was discussed in detail for alkaline phosphatase (Section V.B). In other kinases the phosphoryl transfer occurs directly from the donor to the acceptor in a ternary complex of the enzyme with the two substrates.Often metal ions like magnesium or manganese are needed. These ions interact with the terminal oxygen of the ATP molecule, thus facilitating the nucleophilic attack by the acceptor. The metal ion is often associated with the enzyme. For mechanistic schemes, see the proposed mechanism of action of alkaline phosphatase, especially when a phosphoryl enzyme intermediate is involved. 

Mechanism of action Gemcitabine is a prodrug. Following entry into cells by nucleoside transporters, it is phosphorylated by deoxycytidine kinase and converted to active nucleosides, gemcitabine diphosphate (dFdCDP) and triphosphate (dFdCTP) [36 ]. These metabolites have a synergistic effect dFdCDP inhibits ribonucleotide reductase, which depletes the deoxyribonu-cleotide pools needed for DNA synthesis and enhances incorporation of dFdCTP into DNA [2 ] dFdCTP inhibits DNA polymerase and once incorporated into DNA results in chain termination incorporation of dFdCTP leads to evasion of detection by DNA repair enzymes. 

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