He catalytic activity; replacement of HEPES/KOH buffer with TRIS/HCl

He catalytic activity; replacement of HEPES/KOH buffer with TRIS/HCl abolished the enzymatic activity unless a monovalent cation was present (Figure 3C). Among the cations tested, K+ was 10781694 the most effective (Figure 3C). The K+-dependence of the reaction velocity in the presence of either TRIS/HCl or HEPES/KOH buffers at pH 7.5, is shown in Figure 3D. Maximum activation was reached at different K+ concentrations depending on the buffering species: in TRIS/HCl buffer, 100 mM K+ was the most effective, whereas in HEPES/KOH buffer, maximum activity was reached at about 200 mM K+ concentration. As shown in Figures 3D and 3E, ADPR hydrolysis is significantly affected also by the buffering species present in the reaction mixture. Among the buffers tested at pH 7.5, in theFigure 4. Substrate specificity screening of AtCOG1058 and SoCOG1058/PncC pyrophosphatases. The pyrophosphatase activity of the pure recombinant enzymes was assayed as described in “Materials and Methods”, in the presence of the listed compounds at 0.5 mM concentration each. Abbreviations: Ap3A, diadenosine triphosphate; Ap4A, diadenosine tetraphosphate; Ap5A, diadenosine pentaphosphate; NGD, nicotinamide guanine dinucleotide; NHD, nicotinamide hypoxanthine dinucleotide. doi:10.1371/journal.pone.0065595.gCOG1058 Is a Novel Pyrophosphatase FamilyFigure 5. Kinetic 16985061 characterization of SoCOG1058/PncC and AtCOG1058 enzymes. Plots of the initial velocities of the catalyzed reactions versus substrate concentrations. Kinetic parameters, calculated as described in Materials and Methods, are reported in the table. doi:10.1371/journal.pone.0065595.gpresence of 100 mM K+, TRIS buffer was the best at sustaining activity, followed by MOPS, HEPES, and Phosphate. In the presence of Imidazole and TRICINE, a very low activity was measured (Figure 3E). Optimal pH was Title Loaded From File determined by measuring ADPR hydrolysis in a 50 mM BIS-TRIS/TRIS buffer system at pH values ranging from 5.5 to 8.5. Activity was optimal in a narrow range around pH 7.5 (Figure 3F). The same Co+2-dependence and K+-activation, as well as pH optimum and buffering species dependence, were displayed by the SoCOG1058/PncC enzyme (not shown).Substrate Specificity Screening Reveals that ADP-ribose is the Preferred Substrate of Bacterial COG1058 EnzymesTo get a deeper insight into the COG1058 domain substrate specificity, we performed a detailed in vitro screening of S were removed from culture at days 0, 3, 5, and 7 for flow cytometric several compounds containing a pyrophosphate bond as potential substrates of AtCOG1058 and SoCOG1058/PncC enzymes, by using the assay conditions previously optimized towards ADPR. The results of the screening performed with the two enzymes are shown in Figure 4. Both enzymes display a Co+2-dependent pyrophosphatase activity towards a limited set of substrates, with ADPR being the preferred among the tested compounds. The stand-alone domain also hydrolyzes diadenosine 59-diphosphate (Ap2A) to a significant extent (75 rate with respect to ADPR substrate), and shows some activity with FAD (30 rate), NADH and nicotinate adenine dinucleotide (NaAD) (14 rate). A very low, but still detectable activity is displayed by this enzyme towards NADPH and NAD, while NADP is not a substrate. TheSoCOG1058/PncC bifunctional enzyme is more strictly specific for ADPR; in fact it hydrolyzes Ap2A at about 10 rate with respect to ADPR, while FAD is not a substrate. On the other hand, it behaves similarly to the AtCOG1058 enzyme towards the pyridine dinucleotides. For both enzymes, replacement o.He catalytic activity; replacement of HEPES/KOH buffer with TRIS/HCl abolished the enzymatic activity unless a monovalent cation was present (Figure 3C). Among the cations tested, K+ was 10781694 the most effective (Figure 3C). The K+-dependence of the reaction velocity in the presence of either TRIS/HCl or HEPES/KOH buffers at pH 7.5, is shown in Figure 3D. Maximum activation was reached at different K+ concentrations depending on the buffering species: in TRIS/HCl buffer, 100 mM K+ was the most effective, whereas in HEPES/KOH buffer, maximum activity was reached at about 200 mM K+ concentration. As shown in Figures 3D and 3E, ADPR hydrolysis is significantly affected also by the buffering species present in the reaction mixture. Among the buffers tested at pH 7.5, in theFigure 4. Substrate specificity screening of AtCOG1058 and SoCOG1058/PncC pyrophosphatases. The pyrophosphatase activity of the pure recombinant enzymes was assayed as described in “Materials and Methods”, in the presence of the listed compounds at 0.5 mM concentration each. Abbreviations: Ap3A, diadenosine triphosphate; Ap4A, diadenosine tetraphosphate; Ap5A, diadenosine pentaphosphate; NGD, nicotinamide guanine dinucleotide; NHD, nicotinamide hypoxanthine dinucleotide. doi:10.1371/journal.pone.0065595.gCOG1058 Is a Novel Pyrophosphatase FamilyFigure 5. Kinetic 16985061 characterization of SoCOG1058/PncC and AtCOG1058 enzymes. Plots of the initial velocities of the catalyzed reactions versus substrate concentrations. Kinetic parameters, calculated as described in Materials and Methods, are reported in the table. doi:10.1371/journal.pone.0065595.gpresence of 100 mM K+, TRIS buffer was the best at sustaining activity, followed by MOPS, HEPES, and Phosphate. In the presence of Imidazole and TRICINE, a very low activity was measured (Figure 3E). Optimal pH was determined by measuring ADPR hydrolysis in a 50 mM BIS-TRIS/TRIS buffer system at pH values ranging from 5.5 to 8.5. Activity was optimal in a narrow range around pH 7.5 (Figure 3F). The same Co+2-dependence and K+-activation, as well as pH optimum and buffering species dependence, were displayed by the SoCOG1058/PncC enzyme (not shown).Substrate Specificity Screening Reveals that ADP-ribose is the Preferred Substrate of Bacterial COG1058 EnzymesTo get a deeper insight into the COG1058 domain substrate specificity, we performed a detailed in vitro screening of several compounds containing a pyrophosphate bond as potential substrates of AtCOG1058 and SoCOG1058/PncC enzymes, by using the assay conditions previously optimized towards ADPR. The results of the screening performed with the two enzymes are shown in Figure 4. Both enzymes display a Co+2-dependent pyrophosphatase activity towards a limited set of substrates, with ADPR being the preferred among the tested compounds. The stand-alone domain also hydrolyzes diadenosine 59-diphosphate (Ap2A) to a significant extent (75 rate with respect to ADPR substrate), and shows some activity with FAD (30 rate), NADH and nicotinate adenine dinucleotide (NaAD) (14 rate). A very low, but still detectable activity is displayed by this enzyme towards NADPH and NAD, while NADP is not a substrate. TheSoCOG1058/PncC bifunctional enzyme is more strictly specific for ADPR; in fact it hydrolyzes Ap2A at about 10 rate with respect to ADPR, while FAD is not a substrate. On the other hand, it behaves similarly to the AtCOG1058 enzyme towards the pyridine dinucleotides. For both enzymes, replacement o.

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