Unexpected NADPH Hydratase Activity in the Nitrile Reductase QueF from Escherichia coli

Functional and ligand binding studies of NAD(P)H hydrate dehydratase enzyme from vancomycin-resistant Staphylococcus aureus by NMR spectroscopic approach, including saturation transfer difference (STD-NMR) spectroscopy

NADH and NADPH are labile coenzymes that undergo hydration by enzymatic reaction or by heat at 5,6 double bond, and convert into non-functional hydrates, NADHX and NADPHX, respectively. The NAD(P)H hydrate dehydratase enzyme catalyzes the dehydration of S-NADHX/S-NADPHX at the expense of ATP, and thus contributes in the nicotinamide nucleotide repair process. This enzyme is also known as "metabolite-proofreading enzyme". Herein, we report the molecular cloning and expression of this highly conserved enzyme of vancomycin-resistant Staphylococcus aureus (VRSA). Its functional and inhibition studies were performed for the first time by NMR spectroscopy. NMR studies showed the dehydration of S epimer of NADHX, in the presence of R-NADHX and cyc-NADHX, by NAD(P)H hydrate dehydratase. In addition, by employing the STD-NMR approach, a library of drugs and natural products (total 79) were evaluated for their binding interactions with the NAD(P)H hydrate dehydratase enzyme. Among them, seven compounds showed ligand-like interactions with the enzyme, and thus functional activity of the enzyme was again checked in the presence of each ligand. Compound 2 (Thiamine HCl) was found to fully inhibit the enzyme's function, and recognized as a potential inhibitor. Current study demonstrates that this enzyme deserves further studies as a potential drug target, as its inhibition can disrupt the normal metabolism of pathogenic VRSA.

Unexpected NADPH Hydratase Activity in the Nitrile Reductase QueF from Escherichia coli

The nitrile reductase QueF catalyzes NADPH-dependent reduction of the nitrile group of preQ₀ (7-cyano-7-deazaguanine) into the primary amine of preQ₁ (7-aminomethyl-7-deazaguanine), a biologically unique reaction important in bacterial nucleoside biosynthesis. Here we have discovered that the QueF from Escherichia coli-its D197A and E89L variants in particular (apparent k_cat ≈10^-2  min^-1 )-also catalyze the slow hydration of the C5=C6 double bond of the dihydronicotinamide moiety of NADPH. The enzymatically C6-hydrated NADPH is a 3.5:1 mixture of R and S forms and rearranges spontaneously through anomeric epimerization (β→α) and cyclization at the tetrahydronicotinamide C6 and the ribosyl O2. NADH and 1-methyl- or 1-benzyl-1,4-dihydronicotinamide are not substrates of the enzymatic hydration. Mutagenesis results support a QueF hydratase mechanism, in which Cys190-the essential catalytic nucleophile for nitrile reduction-acts as the general acid for protonation at the dihydronicotinamide C5 of NADPH. Thus, the NADPH hydration in the presence of QueF bears mechanistic resemblance to the C=C double bond hydration in natural hydratases.