title: Mechanistic and structural basis for inhibition of thymidylate synthase ThyX.
abstract: Nature has established two mechanistically and structurally unrelated families of thymidylate synthases that produce de novo thymidylate or dTMP, an essential DNA precursor. Representatives of the alternative flavin-dependent thymidylate synthase family, ThyX, are found in a large number of microbial genomes, but are absent in humans. We have exploited the nucleotide binding pocket of ThyX proteins to identify non-substrate-based tight-binding ThyX inhibitors that inhibited growth of genetically modified Escherichia coli cells dependent on thyX in a manner mimicking a genetic knockout of thymidylate synthase. We also solved the crystal structure of a viral ThyX bound to 2-hydroxy-3-(4-methoxybenzyl)-1,4-naphthoquinone at a resolution of 2.6 Å. This inhibitor was found to bind within the conserved active site of the tetrameric ThyX enzyme, at the interface of two monomers, partially overlapping with the dUMP binding pocket. Our studies provide new chemical tools for investigating the ThyX reaction mechanism and establish a novel mechanistic and structural basis for inhibition of thymidylate synthesis. As essential ThyX proteins are found e.g. in Mycobacterium tuberculosis and Helicobacter pylori, our studies have also potential to pave the way towards the development of new anti-microbial compounds.
authors.affiliation: Laboratoire d'Optique et Biosciences, INSERM U696, CNRS UMR 7645, Ecole Polytechnique, Palaiseau Cedex, Palaiseau 91228, France.
authors.forename: Tamara
authors.initials: T
authors.lastname: Basta
authors.forename: Yap
authors.initials: Y
authors.lastname: Boum
authors.forename: Julien
authors.initials: J
authors.lastname: Briffotaux
authors.forename: Hubert F
authors.initials: HF
authors.lastname: Becker
authors.forename: Isabelle
authors.initials: I
authors.lastname: Lamarre-Jouenne
authors.forename: Jean-Christophe
authors.initials: JC
authors.lastname: Lambry
authors.forename: Stephane
authors.initials: S
authors.lastname: Skouloubris
authors.forename: Ursula
authors.initials: U
authors.lastname: Liebl
authors.forename: Marc
authors.initials: M
authors.lastname: Graille
authors.forename: Herman
authors.initials: H
authors.lastname: van Tilbeurgh
authors.forename: Hannu
authors.initials: H
authors.lastname: Myllykallio
mesh_terms: D000890:Anti-Infective Agents / Q000737:chemistry; D001426:Bacterial Proteins / Q000037:antagonists & inhibitors* / Q000737:chemistry* / Q000235:genetics; D001665:Binding Sites; D002692:Chlamydia trachomatis / Q000201:enzymology* / Q000235:genetics; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics; D016480:Helicobacter pylori / Q000737:chemistry / Q000201:enzymology / Q000235:genetics; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000201:enzymology* / Q000235:genetics; D017434:Protein Structure, Tertiary; D013940:Thymidylate Synthase / Q000037:antagonists & inhibitors* / Q000737:chemistry* / Q000235:genetics
chemical_list: D000890:Anti-Infective Agents; D001426:Bacterial Proteins; D013940:Thymidylate Synthase