10.1021/acscatal.9b05411.s001
Hong Li
Hong
Li
Yongjun Liu
Yongjun
Liu
Mechanistic Investigation of Isonitrile Formation
Catalyzed by the Nonheme Iron/α-KG-Dependent Decarboxylase (ScoE)
American Chemical Society
2020
isonitrile
nonheme
H-abstraction
desaturation
ScoE
electron transfer
Isonitrile Formation Catalyzed
CO
IV
oxidative decarboxylation
QM
2020-02-20 20:12:36
Journal contribution
https://acs.figshare.com/articles/journal_contribution/Mechanistic_Investigation_of_Isonitrile_Formation_Catalyzed_by_the_Nonheme_Iron_-KG-Depcs9b05411endent_Decarboxylase_ScoE_/11852628
Recent structural and biochemical evidence showed that ScoE from Streptomyces coeruleorubidus is a nonheme iron/α-KG-dependent
decarboxylase, which catalyzes the formation of isonitrile group by
desaturation and decarboxylation. This discovery offers an alternative
mechanism for isonitrile formation. The other isonitrile synthases,
such as IsnA, XnPvcA, or AmbI1/AmbI2, convert R–CH(−NH<sub>2</sub>)–CO<sub>2</sub><sup>–</sup> to R–CH(−NC)–CO<sub>2</sub><sup>–</sup> by introducing an additional carbon unit;
however, ScoE catalyzes the conversion of R–NH–CH<sub>2</sub>–CO<sub>2</sub><sup>–</sup> to R–NC
through oxidative decarboxylation. To explore the catalytic mechanism
of ScoE, on the basis of the high-resolution crystal structure, the
enzyme–substrate complex models were constructed and a series
of combined QM/MM calculations were performed. Our results reveal
that the ScoE-catalyzed reaction contains two decoupled parts, desaturation
and decarboxylation. The Fe<sup>IV</sup>-oxo-triggered desaturation
includes two consecutive H-abstractions, which are similar to the
C–C single bond desaturation catalyzed by other nonheme iron/α-KG-dependent
desaturases. In the second stage reaction, the decarboxylation of
the substrate radical generated by H-abstraction was calculated to
be quite easy, whereas the previously proposed decarboxylation that
involves the hydroxylated intermediate was calculated to be difficult.
Importantly, the electron transfer from the substrate to the iron
center is the key factor for lowering the barrier of decarboxylation.
Thus, the central iron ion is not only responsible for H-abstraction
but also acts as an electron relay station for decarboxylation. In
addition, this electron transfer was found to be coupled with a proton
transfer, in which R310 and the associated H-bonding network play
a critical role. In general, the first C–N desaturation is
the rate-limiting step of the whole catalysis with an overall energy
barrier of 17.6 or 16.9 kcal/mol in two competitive pathways, qualitatively
agreeing with the estimated free energy (17.9–18.1 kcal/mol)
from experiments. These results may provide useful information for
understanding the biosynthesis of isonitrile and the oxidative decarboxylation
catalyzed by nonheme iron/α-KG-dependent enzymes.