X-ray, NMR, and mutational studies of the catalytic cycle of the GDP-mannose mannosyl hydrolase reaction

GDP-mannose hydrolase catalyzes the hydrolysis with inversion of GDP-α-D-hexose to GDP and β-D-hexose by nucleophilic substitution by water at C1 of the sugar. Two new crystal structures (free enzyme and enzyme-substrate complex), NMR, and site-directed mutagenesis data, combined with the structure of the enzyme-product complex reported earlier, suggest a four-stage catalytic cycle. An important loop (L6, residues 119-125) contains a ligand to the essential Mg²⁺ (Gln-123), the catalytic base (His-124), and three anionic residues. This loop is not ordered in the X-ray structure of the free enzyme due to dynamic disorder, as indicated by the two-dimensional ¹H-¹⁵N HMQC spectrum, which shows selective exchange broadening of the imidazole nitrogen resonances of His-124 (k_ex = 6.6 × 10⁴ s^-1). The structure of the enzyme-Mg ²⁺-GDP-mannose substrate complex of the less active Y103F mutant shows loop L6 in an open conformation, while the structure of the enzyme-Mg ²⁺-GDP product complex showed loop L6 in a closed, "active" conformation. ¹H-¹⁵N HMQC spectra show the imidazole Nε of His-124 to be unprotonated, appropriate for general base catalysis. Substituting Mg²⁺ with the more electrophilic metal ions Mn ²⁺ or Co²⁺ decreases the pK_a in the pH versus k_cat rate profiles, showing that deprotonation of a metal-bound water is partially rate-limiting. The H124Q mutation, which decreases k_cat 10^3.4-fold and largely abolishes its pH dependence, is rescued by the Y103F mutation, which increases k_cat 23-fold and restores its pH dependence. The structural basis of the rescue is the fact that the Y103F mutation shifts the conformational equilibrium to the open form moving loop L6 out of the active site, thus permitting direct access of the specific base hydroxide from the solvent. In the proposed dissociative transition state, which occurs in the closed, active conformation of the enzyme, the partial negative charge of the GDP leaving group is compensated by the Mg²⁺, and by the closing of loop L2 that brings Arg-37 closer to the β-phosphate. The development of a positive charge at mannosyl C1, as the oxocarbenium-like transition state is approached, is compensated by closing the anionic loop, L6, onto the active site, further stabilizing the transition state.