The mechanism of phosphoryl transfer reaction and the role of active site residues on the basis of ribokinase-like kinases

Abstract

The role of ribokinase-like carbohydrate kinases consists in ATP dependent phosphorylation of small molecules containing hydroxymethyl group. Although they differ substantially in structural terms and exhibit a broad substrate specificity, some family-wide conserved features can be distinguished suggesting the common mode of action. 4-methyl-5-β-hydroxyethylthiazole kinase (Thz kinase) was chosen as a representative model and the mechanism proposed in X-ray crystal structure paper provided the basis for calculations. In particular, the possible role of several active site residues (Arg121 and Cys198 among others) and of the two magnesium ions was examined. Static and dynamic catalytic fields for the reaction were generated revealing the most favourable environment for the preferential transition state stabilization. An attempt to model the phosphoryl transfer reaction as well as to investigate the influence of the cysteine residue on the reaction course at the semiempirical PM3 level of theory was undertaken.