Biosynthesis of the DNA base thymine depends on activity of the enzyme
thymidylate synthase (TS) to catalyze the methylation of the uracil moiety of
2’-deoxyuridine-5’-monophosphate (dUMP). All known thymidylate
synthases (TSs) rely on an active site residue of the enzyme to activate
dUMP1, 2. This functionality has been demonstrated for classical TSs,
including human TS, and is instrumental in mechanism-based inhibition of these
enzymes. Here we report the first example of thymidylate biosynthesis that
occurs without an enzymatic nucleophile. This unusual biosynthetic pathway
occurs in organisms containing the thyX gene, which codes for a
flavin-dependent thymidylate synthase (FDTS), and is present in several human
pathogens3–5. Our findings indicate that the putative
active site nucleophile is not required for FDTS catalysis, and no alternative
nucleophilic residues capable of serving this function can be identified.
Instead, our findings suggest that a hydride equivalent (i.e. a proton and two
electrons) is transferred from the reduced flavin cofactor directly to the
uracil ring, followed by an isomerization of the intermediate to form the
product, 2’-deoxythymidine-5’-monophosphate (dTMP). These
observations indicate a very different chemical cascade than that of classical
TSs or any other known biological methylation. The findings and chemical
mechanism proposed here, together with available structural data, suggest that
selective inhibition of FDTSs, with little effect on human thymine biosynthesis,
should be feasible. Since several human pathogens depend on FDTS for DNA
biosynthesis, its unique mechanism makes it an attractive target for antibiotic
drugs.