Dihydropyrimidine dehydrogenase (DPD) catalyzes the reduction of uracil and thymine bases with electrons derived from NADPH. The mammalian DPD enzyme is a functional homodimer and has an elaborate cofactor arrangement. Two flavin cofactors (FAD and FMN) reside in two active site cavities that are separated by around 60 Å. The flavins are apparently bridged by four Fe4S4 clusters, two of which are provided by the partner protomer of the dimer. The study of DPD has been hampered by modest yield from both native sources and from heterologous expression in E. coli. In addition, minimal active enzyme is obtained when the DPD gene is fused to an N-terminal 6His-tag. This limitation has dictated the use of traditional purification methods that are made more challenging by apparent over-expression of truncated and/or non-active forms of DPD. Here we detail methods of expression and purification that result in a ~4-fold improvement in the yield of active porcine DPD when expressed in E. coli BL21 DE3 cells via the pET plasmid expression system. The addition of ferrous ions and sulfate during induction provide a small increase in purified active enzyme. However, the addition of FAD and FMN during cell lysis results in a substantial increase in activity that also reduces the relative proportion of non-active, high molecular weight protein contaminants. We also describe methods that permit correlation of the flavin content with the amount of active enzyme and thus permit simple, rapid quantitation and evaluation of purified DPD sample.
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