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

Maria A. Schumacher, Darrick Carter, Daniel M. Scott, David S. Roos, Buddy Ullman, Richard G. Brennan

Research output: Contribution to journalArticle

60 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)3219-3232
Number of pages14
JournalEMBO Journal
Volume17
Issue number12
DOIs
StatePublished - Jun 15 1998

Fingerprint

uracil phosphoribosyltransferase
Toxoplasma
Prodrugs
Uracil
Crystal structure
Drug Design
Hydrogen
Hydrogen bonds
Phosphoribosyl Pyrophosphate
Uridine Monophosphate
Antiparasitic Agents
Pyrimidines
Thymine
Fluorine
Water
Cytosine
Toxoplasmosis
Pathogens
Substrates
Fluorouracil

Keywords

  • Crystallography
  • Structure-based drug design
  • Toxoplasma gondii
  • Toxoplasmosis
  • Uracil phosphoribosyltransferase

ASJC Scopus subject areas

  • Genetics
  • Cell Biology

Cite this

Crystal structures of Toxoplasma gondii uracil phosphoribosyltransferase reveal the atomic basis of pyrimidine discrimination and prodrug binding. / Schumacher, Maria A.; Carter, Darrick; Scott, Daniel M.; Roos, David S.; Ullman, Buddy; Brennan, Richard G.

In: EMBO Journal, Vol. 17, No. 12, 15.06.1998, p. 3219-3232.

Research output: Contribution to journalArticle

Schumacher, Maria A. ; Carter, Darrick ; Scott, Daniel M. ; Roos, David S. ; Ullman, Buddy ; Brennan, Richard G. / Crystal structures of Toxoplasma gondii uracil phosphoribosyltransferase reveal the atomic basis of pyrimidine discrimination and prodrug binding. In: EMBO Journal. 1998 ; Vol. 17, No. 12. pp. 3219-3232.
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abstract = "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 {\AA} resolution), the UPRTase bound to its substrate, uracil (2.2 {\AA} resolution), its product, UMP (2.5 {\AA} resolution), and the prodrug, 5-fluorouracil (2.3 {\AA} 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.",
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