Mechanism of Mg2+-Accompanied Product Release in Sugar Nucleotidyltransferases.

The nucleotidyl transfer reaction, catalyzed by sugar
nucleotidyltransferases (SNTs), is assisted by two
active site Mg2+ ions. While studying this reaction using
X-ray crystallography, we captured snapshots of
the pyrophosphate (product) as it exits along a
pocket. Surprisingly, one of the active site Mg2+
ions remains coordinated to the exiting pyrophosphate.
This hints at the participation of Mg2+ in the
process of product release, besides its role in catalyzing
nucleotidyl transfer. These observations are
further supported by enhanced sampling molecular
dynamics simulations. Free energy computations
suggest that the product release is likely to be rate
limiting in SNTs, and the origin of the high free energy
barrier for product release could be traced back to
the ‘‘slow’’ conformational change of an Arg residue
at the exit end of the pocket. These results establish
a dual role for Mg2+, and propose a general mechanism
of product release during the nucleotidyl transfer
by SNTs.