research papers
dUTP pyrophosphatase (dUTPase) cleaves the α-β phosphodiester of dUTP to form pyrophosphate and dUMP, preventing incorporation of uracil into DNA and providing the substrate for thymine synthesis. Seven crystal structures of feline immunodeficiency virus (FIV) dUTPase in three crystal forms have been determined, including complexes with substrate (dUTP), product (dUMP) or inhibitor (dUDP) bound. The native enzyme has been refined at 1.40 Å resolution in a hexagonal crystal form and at 2.3 Å resolution in an orthorhombic crystal form. In the dUDP complex in a cubic crystal form refined at 2.5 Å resolution, the C-terminal conserved P-loop motif is fully ordered. The analysis defines the roles of five sequence motifs in interaction with uracil, deoxyribose and the α-, β- and γ-phosphates. The enzyme utilizes adaptive recognition to bind the α- and β-phosphates. In particular, the α-β phosphodiester adopts an unfavorable eclipsed conformation in the presence of the P-loop. This conformation may be relevant to the mechanism of α-β phosphodiester bond cleavage.
Keywords: dUTP pyrophosphatase.
Supporting information
PDB references: P63 native dUTPase, 1f7d; P63 dUMP complex, 1f7k; P63 dUMP complex (from dUTP), 1f7n; P212121 native dUTPase, 1f7o; P212121 dUDP complex, 1f7p; P212121 dUTP complex, 1f7q; P213 dUDP complex, 1f7r