Kinetic Mechanism of Human dUTPase, an Essential Nucleotide Pyrophosphatase Enzyme

Abstract

Human dUTPase is essential in controlling relative cellular levels of dTTP/dUTP, both of which can be incorporated into DNA. The nuclear isoform of the enzyme has been proposed as a promising novel target for anticancer chemotherapeutic strategies. The recently determined three-dimensional structure of this protein in complex with an isosteric substrate analogue allowed in-depth structural characterization of the active site. However, fundamental steps of the dUTPase enzymatic cycle have not yet been revealed. This knowledge is indispensable for a functional understanding of the molecular mechanism and can also contribute to the design of potential antagonists. Here we present detailed pre-steady-state and steady-state kinetic investigations using a single tryptophan fluorophore engineered into the active site of human dUTPase. This sensor allowed distinction of the apoenzyme, enzyme-substrate, and enzymeproduct complexes. We show that the dUTP hydrolysis cycle consists of at least four distinct enzymatic steps: (i) fast substrate binding, (ii) isomerization of the enzyme-substrate complex into the catalytically competent conformation, (iii) a hydrolysis (chemical) step, and (iv) rapid, nonordered release of the products. Independent quenched-flow experiments indicate that the chemical step is the rate-limiting step of the enzymatic cycle. To follow the reaction in the quenched-flow, we devised a novel method to synthesize ␥-32 P-labeled dUTP. We also determined by indicator-based rapid kinetic assays that proton release is concomitant with the rate-limiting hydrolysis step. Our results led to a quantitative kinetic model of the human dUTPase catalytic cycle and to direct assessment of relative flexibilities of the C-terminal arm, critical for enzyme activity, in the enzyme-ligand complexes along the reaction pathway.dUTPase is the unique enzyme that specifically hydrolyzes the ␣-␤ pyrophosphate bond of dUTP to yield dUMP and PP i(1). The enzyme is essential in maintaining DNA integrity in dividing cells (2, 3). Its activity is responsible for setting the physiological dUTP/dTTP concentration ratios (1:24) (4), thus preventing high rates of uracil incorporation into newly synthesized DNA. Although uracil in DNA is tolerated to a certain level by the base excision DNA repair mechanisms, higher levels of uracil in DNA trigger double-strand breaks and lead to cell death (5). Several lines of evidence show that up-regulated dUTPase is responsible for desensitizing tumors to drugs inhibiting the thymidylate synthase pathway, thus acting as an important survival factor for tumor cells (6, 7). Increased levels of the nuclear isoform of the enzyme correlate to worsened prognosis of several tumors, as revealed by detailed analysis of tissue samples (8, 9). dUTPase has therefore emerged as a high potential anticancer drug target, which possesses several additional, possibly advantageous features for drug design. Unlike most nucleotide-metabolizing enzymes, dUTPase is extremely specific to its substrate nucleotide, potenti...

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