Structures of feline immunodeficiency virus dUTP pyrophosphatase and its nucleotide complexes in three crystal forms

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.