An unusual mechanism of thymidylate biosynthesis in organisms containing the thyX gene

Abstract

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.