Solution structure and mechanism of the MutT pyrophosphohydrolase

The MutT enzyme prevents errors in DNA replication by hydrolyzing mutagenic nucleotide substrates such as 8-oxo-dGTP. It does so by catalyzing nucleophilic attack at the electron rich P beta of nucleoside triphosphates. Members of this small mechanistic class of enzymes require two divalent cations per active site for activity--one coordinated by the enzyme and the other by the enzyme-bound NTP--and show low catalytic powers of 10(7)- to 10(9)-fold. The first structure of an enzyme of this class, obtained by NMR methods in solution, shows MutT to be a compact globular protein with an alpha + beta-fold. The binding of the essential divalent cation activator Mg2+ and the substrate analog Mg(2+)-AMPCPP to the MutT enzyme to form the quaternary E-Mg(2+)-AMPCPP-Mg2+ complex does not alter the global fold of the enzyme but produces localized small conformational changes at or near the metal and substrate binding sites. The adenine-ribose moiety binds in a hydrophobic cleft near 3-strands of a mixed beta-sheet, with the 6-NH2 group of the purine ring approaching the -NH2 side chain of Asn-119. With a 6-keto group, GTP would interact more favorably with Asn-119, consistent with the substrate preference of MutT for guanine over adenine nucleotides. The enzyme-bound metal is coordinated by three conserved Glu residues (Glu-56, Glu-57, and Glu-98), the backbone carbonyl of a conserved Gly residue (Gly-38), and by two water ligands. The metal-triphosphate moiety of the metal-AMPCPP complex binds in the second coordination sphere of the enzyme-bound divalent cation. One of the water ligands of the enzyme-bound metal ion is well positioned to attack P beta with inversion and to be deprotonated or oriented by Glu-53, which in turn may be oriented by Arg-52. Lys-39 is positioned to interact electrostatically with the alpha-phosphoryl group and thereby to facilitate the departure of the NMP-leaving group. Quantitatively, the 10(9)-fold rate acceleration produced by the MutT enzyme may be ascribed to catalysis by approximation and polarization of the attacking water by the enzyme-bound metal ion (> or = 10(5)-fold), activation of the NMP leaving group by Lys-39 (10-fold), charge neutralization at P beta by the nucleotide-bound divalent cation (> or = 10-fold), and orientation and/or deprotonation of the attacking water by Glu-53 (> or = 10(2)-fold). This reaction mechanism, derived from the solution structure of the quaternary MutT complex, is both qualitatively and quantitatively consistent with the results of mutagenesis studies and may well be applicable to other enzymes that catalyze nucleophilic substitution at the electron-rich P beta of NTP substrates.