ci9b00837_si_001.pdf (1.67 MB)
Mechanism of Uncoupled Carbocyclization and Epimerization Catalyzed by Two Non-Heme Iron/α-Ketoglutarate Dependent Enzymes
journal contribution
posted on 2019-12-12, 14:33 authored by Hong Li, Wenyou Zhu, Yongjun LiuThe non-heme iron/α-ketoglutarate dependent enzymes
SnoK
and SnoN from Streptomyces nogalater are involved
in the biosynthesis of anthracycline nogalamycin. Although they have
similar active sites, SnoK is responsible for carbocyclization whereas
SnoN solely catalyzes the hydroxyl epimerization. Herein, we performed
docking, molecular simulations, and a series of combined quantum mechanics
and molecular mechanics (QM/MM) calculations to illuminate the mechanisms
of two enzymes. The catalytic reactions of two enzymes occur on the
quintet state surface. For SnoK, the whole reaction includes two separated
hydrogen-abstraction steps and one radical addition, and the latter
step is calculated to be rate limiting with an energy barrier of 21.7
kcal/mol. Residue D106 is confirmed to participate in the construction
of the hydrogen bond network, which plays a crucial role in positioning
the bulky substrate in a specific orientation. Moreover, it is found
that SnoN is only responsible for the hydrogen abstraction of the
intermediate, and no residue was suggested to be suitable for donating
a hydrogen atom to the substrate radical, which further confirms the
suggestion based on experiments that either a cellular reductant or
another enzyme protein could donate a hydrogen atom to the substrate.
Our docking results coincide with the previous structural study that
the different roles of two enzymes are achieved by minor changes in
the alignment of the substrates in front of the reactive ferryl-oxo
species. This work highlights the reaction mechanisms catalyzed by
SnoK and SnoN, which is helpful for engineering the enzymes for the
biosynthesis of anthracycline nogalamycin.