Differences in the Nature of the Phosphoryl Transfer Transition State in Protein Phosphatase 1 and Alkaline Phosphatase: Insights from QM Cluster Models

Quantum mechanical (QM) cluster models
are used to probe effects
on the catalytic properties of protein phosphatase 1 (PP1) and alkaline
phosphatase (AP) due to metal ions and active site residues. The calculations
suggest that the phosphoryl transfer transition states in PP1 are
synchronous in nature with a significant degree of P–Olg cleavage, while those in AP are tighter with a modest degree
of P–Olg cleavage and a range of P–Onuc formation. Similar to observations made in our recent work,
a significant degree of cross talk between the forming and breaking
P–O bonds complicates the interpretation of the Brønsted
relation, especially in regard to AP for which the computed βlg/βEQ,lg value does not correlate with the
degree of P–Olg cleavage regardless of the metal
ions in the active site. By comparison, the correlation between βlg/βEQ,lg and the P–Olg bond
order is more applicable to PP1, which generally exhibits less variation
in the transition state than AP. Results for computational models
with swapped metal ions between PP1 and AP suggest that the metal
ions modulate both the nature of the transition state and the degrees
of sensitivity of the transition state to the leaving group. In the
reactant state, the degree of the scissile bond polarization is also
different in the two enzymes, although this difference appears to
be largely determined by the active site residues rather than the
metal ions. Therefore, both the identity of the metal ion and the
positioning of polar or charged residues in the active site contribute
to the distinct catalytic characteristics of these enzymes. Several
discrepancies observed between the QM cluster results and the available
experimental data highlight the need for further QM/MM method developments
for the quantitative analysis of metalloenzymes that contain open-shell
transition metal ions.