(KARI)
catalyzes the conversion of (S)-2-acetolactate
or (S)-2-aceto-2-hydroxybutyrate to 2,3-dihydroxy-3-alkylbutyrate,
the second step in the biosynthesis of branched chain amino acids
(BCAAs). Because the BCAA biosynthetic pathway is present in bacteria,
plants, and fungi, but absent in animals, it is an excellent target
for the development of new-generation antibiotics and herbicides.
Nevertheless, the mechanism of the KARI-catalyzed reaction has not
yet been fully solved. In this study, we used iterative molecular
dynamics (MD) flexible fitting–Rosetta techniques to optimize
the three-dimensional solution structure of archaea KARI from Sulfolobus solfataricus (Sso-KARI) determined from
cryo-electron microscopy. On the basis of the structure of the Sso-KARI/2Mg2+/NADH/(S)-2-acetolactate complex, we deciphered
the catalytic mechanism of the KARI-mediated reaction through hybrid
quantum mechanics/molecular mechanics MD simulations in conjunction
with umbrella sampling. With an activation energy of only 6.06 kcal/mol,
a water-mediated, metal-catalyzed, base-induced (WMMCBI) mechanism
was preferred for deprotonation of the tertiary OH group of (S)-2-acetolactate in Sso-KARI. The WMMCBI mechanism for
double proton transfer occurred within a proton wire route with two
steps involving the formation of hydroxide: (i) Glu233 served as a
general base to deprotonate the Mg2+-bound water, forming
a hydroxide-coordinated Mg2+ ion; (ii) this hydroxide ion
acted as a strong base that rapidly deprotonated the ternary OH group
of the substrate. In contrast, the direct deprotonation of the substrate
by Glu233 was kinetically unfavorable. This mechanism suggests a novel
approach for designing catalysts for deprotonation and provides clues
for the development of new-generation antibiotics and herbicides.