Crystal structures of Toxoplasma gondii uracil phosphoribosyltransferase reveal the atomic basis of pyrimidine discrimination and prodrug binding

Uracil phosphoribosyltransferase (UPRTase) catalyzes the transfer of a ribosyl phosphate group from α‐D‐5‐phosphoribosyl‐1‐pyrophosphate to the N1 nitrogen of uracil. The UPRTase from the opportunistic pathogen Toxoplasma gondii is a rational target for antiparasitic drug design. To aid in structure‐based drug design studies against toxoplasmosis, the crystal structures of the T.gondii apo UPRTase (1.93 Å resolution), the UPRTase bound to its substrate, uracil (2.2 Å resolution), its product, UMP (2.5 Å resolution), and the prodrug, 5‐fluorouracil (2.3 Å resolution), have been determined. These structures reveal that UPRTase recognizes uracil through polypeptide backbone hydrogen bonds to the uracil exocyclic O2 and endocyclic N3 atoms and a backbone–water–exocyclic O4 oxygen hydrogen bond. This stereochemical arrangement and the architecture of the uracil‐binding pocket reveal why cytosine and pyrimidines with exocyclic substituents at ring position 5 larger than fluorine, including thymine, cannot bind to the enzyme. Strikingly, the T.gondii UPRTase contains a 22 residue insertion within the conserved PRTase fold that forms an extended antiparallel β‐arm. Leu92, at the tip of this arm, functions to cap the active site of its dimer mate, thereby inhibiting the escape of the substrate‐binding water molecule.