1syn
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E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH BW1843U89 AND 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)
OverviewOverview
BACKGROUND: Thymidylate synthase (TS) is critical to DNA synthesis as it, catalyzes the rate limiting step in the only biosynthetic pathway for, deoxythymidine monophosphate (dTMP) production. TS is therefore an, important target for anti-proliferative and anti-cancer drug design. The, TS enzymatic mechanism involves the reductive methylation of the, substrate, deoxyuridine monophosphate (dUMP), by transfer of a methylene, group from the co-factor, methylenetetrahydrofolate (CH2H4folate), resulting in the production of deoxythymidine monophosphate (dTMP) and, dihydrofolate (H2folate). Previous drug design efforts based on co-factor, analogues have produced good inhibitors of TS, but poor bioavailability, and toxicity have limited their usefulness. BW1843U89, a folate analogue, is a recently developed compound which is an exceptionally strong, inhibitor (Ki = 0.09 nM), has good bioavailability and in clinical trials, thus far has not demonstrated significant toxicity. RESULTS: We report the, crystal structure of E. coli TS in ternary complex with dUMP and BW1843U89, at 2.0 A resolution. Although the benzoquinazoline ring system of the, inhibitor binds to TS in much the same manner as previously determined for, H2folate and CB3717, the larger size of the ligand is accommodated by the, enzyme through a local distortion of the active site, that is not strictly, conserved in both monomers in the asymmetric unit. Several conserved, waters that had been previously implicated in mechanistic roles have been, displaced. CONCLUSIONS: BW1843U89 forms a ternary complex with dUMP and, completes with CH2H4 folate at the active site. Inhibition of TS by, BW1843U89 shows four unique aspects in its mechanism of action. BW1843U89, prevents the Michael addition of dUMP to Cys146, in contrast to the, mechanisms implicated from crystallography of other quinazoline based, inhibitors; displaces a catalytic water from the active site; reorders a, peptide loop (Leu72-Trp83) in the active site; and is unique amongst the, antifolates in inactivating TS at a stoichiometric ratio of one molecule, per TS dimer. Thus, it exploits the principles of negative cooperativity, that are increasingly being recognized in the catalytic mechanism of the, enzyme per se. The structure suggests that this 'half-the-sites' effect is, catalytic and not related to ligand binding. Therefore BW1843U89 is both a, competitive inhibitor (at the binding site) and a non-competitive, inhibitor at the other site.
About this StructureAbout this Structure
1SYN is a Single protein structure of sequence from Escherichia coli with UMP and F89 as ligands. Active as Thymidylate synthase, with EC number 2.1.1.45 Full crystallographic information is available from OCA.
ReferenceReference
The complex of the anti-cancer therapeutic, BW1843U89, with thymidylate synthase at 2.0 A resolution: implications for a new mode of inhibition., Stout TJ, Stroud RM, Structure. 1996 Jan 15;4(1):67-77. PMID:8805515
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