Catalytic and structural role of the metal ion in dUTP pyrophosphatase

The metal ion dependence of the catalytic activity of recombinant Escherichia coli dUTP pyrophosphatase (dUTPase), an essential enzyme preventing incorporation of uracil into DNA, has been investigated by steady-state kinetic, electron paramagnetic resonance, and electron nuclear double resonance methods. Values of k(cat) and k(cat)K(m) were 4.5 +/- 0.1 s(-1) and 0.49 +/- 0.1 x 10(6) M(-1).s(-1) in the absence of divalent metal ions, 14.7 +/- 2.2 s(-1) and 25.1 +/- 7.4 x 10(6) M(-1).s(-1) in the presence of Mg(2+) or Mn(2+), and 24.2 +/- 3.6 s(-1) and 2.4 +/- 0.7 x 10(6) M(-1).s(-1) when supported by VO(2+) or bis(acetylacetonato)oxovanadium(IV). Binding of VO(2+) to the enzyme in the presence of dUDP, a nonhydrolyzable substrate analog, was specific and competitive with Mg(2+). Electron paramagnetic resonance spectra of the ternary enzyme-VO(2+)-chelate-dUDP complex revealed a pattern of (31)P superhyperfine coupling specifying two structurally equivalent phosphate groups equatorially coordinated to the VO(2+) ion. Proton electron nuclear double resonance spectra revealed an equatorial acetylacetonate ligand, indicating that one of the organic ligands had been displaced. By molecular graphics modeling, we show that the diphosphate group of enzyme-bound dUDP is sterically accessible to a hemi-chelate form of VO(2+). We propose a similar location compatible with all kinetic and spectroscopic results to account for the reactivity of VO(2+) and the VO(2+)-chelate in dUTP hydrolysis. In this location the metal ion could promote an ordered conformation of the C-terminal fragment that is obligatory for catalysis but dynamically flexible in the free enzyme.