Mechanistic and In silico Characterization of Metal ion Requirements of Escherichia coli Zinc Phosphodiesterase Activity

Zinc phosphodiesterase (ZiPD) participates in the maturation of tRNA precursors. The roles of metal ions in promoting phosphoryl transfer reaction on zinc phosphodiesterase (ZiPD) activity have not been fully characterized. Therefore, this study investigated the effects of some metal ions on phosphodiesterase activity of Escherichia coli ZiPD as well as the binding site and binding affinity of the metal ions. ZiPD activity was measured by monitoring the rate of hydrolysis of bis-para-nitrophenyl phosphate (bis-pNPP) in the presence of some selected divalent metal ions (Mn²⁺, Co²⁺, Mg²⁺ and Zn²⁺). The results obtained revealed that Mn²⁺ at 1 mM activated ZiPD activity by 4-fold with binding affinity score of 1.795. Co²⁺ at 0.5 mM activated ZiPD activity by 2-fold with binding affinity score of 1.773. Mg²⁺ at 0.5 mM enhanced the binding affinity of ZiPD for bis-pNPP but did not increase the turnover rate of ZiPD. Zn²⁺ at 1.5 mM activated ZiPD activity by 2-fold via increased affinity of ZiPD for bis-pNPP. In conclusion, the findings from this study showed that Mn²⁺ and Zn²⁺ are the most effective stimulatory ions of ZiPD for bis-pNPP while Zn²⁺ exerted the highest binding affinity of ZiPD for bis-pNPP.