The
native function of dihydropyrimidine dehydrogenase (DPD) is
to reduce the 5,6-vinylic bond of pyrimidines uracil and thymine with
electrons obtained from NADPH. NADPH and pyrimidines bind at separate
active sites separated by ∼60 Å that are bridged by four
Fe4S4 centers. We have shown that DPD undergoes
reductive activation, taking up two electrons from NADPH [Beaupre,
B. A., et al. (2020) Biochemistry 59, 2419–2431].
pH studies indicate that the rate of turnover is not controlled by
the protonation state of the general acid, cysteine 671. The activation
of the C671 variants is delineated into two phases particularly at
low pH values. Spectral deconvolution of the delineated reductive
activation reaction reveals that the initial phase results in the
accumulation of charge transfer absorption added to the binding difference
spectrum for NADPH. The second phase results in reduction of one of
the two flavins. X-ray crystal structure analysis of the C671S variant
soaked with NADPH and the slow substrate, thymine, in a low-oxygen
atmosphere resolved the presumed activated form of the enzyme that
has the FMN cofactor reduced. These data reveal that charge transfer
arises from the proximity of the NADPH and FAD bases and that the
ensuing flavin is a result of rapid transfer of electrons to the FMN
without accumulation of reduced forms of the FAD or Fe4S4 centers. These data suggest that the slow rate of turnover
of DPD is governed by the movement of a mobile structural feature
that carries the C671 residue.