F the ADP-linked ribose with mannose significantly decreases the activity, which is further decreased or completely abolished when ribose is replaced by glucose (Figure 4). A very low activity is displayed by the AtCOG1058 Title Loaded From File enzyme towards GDP-mannose, while GDP-glucose is not recognized by either protein. The presence of a phosphate group on the adenine-linked ribose significantly decreases or fully abolishes the activity. As to the ApnA series, for both enzymes the activity falls off when n .2. ATP is hydrolyzed to AMP only by the AtCOG1058 protein and to a very low extent (Figure 4). Neither enzyme is able to hydrolyze the pyrophosphate bond in ribonucleoside Title Loaded From File diphosphates (not shown). Results of the kinetic analyses for the preferred substrates are reported in Figure 5. Although the AtCOG1058 enzyme hydrolyzes ADPR and Ap2A at similar rates, the catalytic efficiency (kcat/Km) towards ADPR is about 14 fold higher. In addition, the bifunctional enzyme is about seven-fold less efficient towards ADPR than the stand-alone pyrophosphatase. Neither enzyme is able to remove a phosphate group from ribonucleoside mono- and diphosphates or from NADP, nor to hydrolyze the phosphodiester bond in 29, 39- and 39, 59-cyclic nucleotides (not shown).COG1058 Is a Novel Pyrophosphatase FamilyFigure 6. Phylogenetic distribution and domain composition of COG1058. Schematic representation of bacterial (A), eukaryotic (B) and archaeal (C) species trees showing COG1058 genes mapping. Green circle designates the COG1058 gene; the FAD synthase gene is represented by a red circle; the fused COG1058/pncC gene is shown as a blue square. Numbers within squares represents the number of gene copies per genome. doi:10.1371/journal.pone.0065595.gCOG1058 Is a Novel Pyrophosphatase FamilyFigure 7. Phylogenetic tree of COG1058. Schematic representation of the COG1058 phylogenetic tree (full version is in Fig. S1). The stand-alone COG1058 gene and the gene fused with FAD synthetase and pncC genes are depicted as green, red and blue circles, respectively. The Shewanella oneidensis and Agrobacterium tumefaciens COG1058 proteins, experimentally characterized in this work, are marked by red stars. Thermoplasma acidophilum COG1058 protein, whose 3D structure is available, is highlighted. doi:10.1371/journal.pone.0065595.gCOG1058 Phylogenetic Analysis Reveals a Wide Distribution and Fusion with Different Catalytic DomainsAnalysis of the phylogenetic distribution of COG1058 members in the three kingdoms of life revealed that they are widely distributed, occurring in approximately half of the eukaryotic, bacterial, and archaeal genomes (Figure 6). The COG1058 domain can be found either as a stand-alone domain, or in a fused form with NMN deamidase or FAD synthase (that catalyzes FMN adenylylation to FAD). In particular, in archaea, in a- and some d-proteobacteria, the COG1058 domain occurs only as a single domain, while in remaining bacterial taxonomic groups it is mostly found fused with PncC (Figure 6A ). Eukaryotes have both single- and two-domain proteins, the latter being composed of the COG1058 domain fused to FAD synthase (Figure 6B). While the single-domain form is mostly present in fungi, the fused form is widely distributed among plants and animals. Notably, in plants the COG1058 domain is located at the N-terminus, whereas in animals it occurs at the C-terminus. The large-scaletopology of the COG1058 phylogenetic tree (Figure 7, and Figure S1) is largely consistent with.F the ADP-linked ribose with mannose significantly decreases the activity, which is further decreased or completely abolished when ribose is replaced by glucose (Figure 4). A very low activity is displayed by the AtCOG1058 enzyme towards GDP-mannose, while GDP-glucose is not recognized by either protein. The presence of a phosphate group on the adenine-linked ribose significantly decreases or fully abolishes the activity. As to the ApnA series, for both enzymes the activity falls off when n .2. ATP is hydrolyzed to AMP only by the AtCOG1058 protein and to a very low extent (Figure 4). Neither enzyme is able to hydrolyze the pyrophosphate bond in ribonucleoside diphosphates (not shown). Results of the kinetic analyses for the preferred substrates are reported in Figure 5. Although the AtCOG1058 enzyme hydrolyzes ADPR and Ap2A at similar rates, the catalytic efficiency (kcat/Km) towards ADPR is about 14 fold higher. In addition, the bifunctional enzyme is about seven-fold less efficient towards ADPR than the stand-alone pyrophosphatase. Neither enzyme is able to remove a phosphate group from ribonucleoside mono- and diphosphates or from NADP, nor to hydrolyze the phosphodiester bond in 29, 39- and 39, 59-cyclic nucleotides (not shown).COG1058 Is a Novel Pyrophosphatase FamilyFigure 6. Phylogenetic distribution and domain composition of COG1058. Schematic representation of bacterial (A), eukaryotic (B) and archaeal (C) species trees showing COG1058 genes mapping. Green circle designates the COG1058 gene; the FAD synthase gene is represented by a red circle; the fused COG1058/pncC gene is shown as a blue square. Numbers within squares represents the number of gene copies per genome. doi:10.1371/journal.pone.0065595.gCOG1058 Is a Novel Pyrophosphatase FamilyFigure 7. Phylogenetic tree of COG1058. Schematic representation of the COG1058 phylogenetic tree (full version is in Fig. S1). The stand-alone COG1058 gene and the gene fused with FAD synthetase and pncC genes are depicted as green, red and blue circles, respectively. The Shewanella oneidensis and Agrobacterium tumefaciens COG1058 proteins, experimentally characterized in this work, are marked by red stars. Thermoplasma acidophilum COG1058 protein, whose 3D structure is available, is highlighted. doi:10.1371/journal.pone.0065595.gCOG1058 Phylogenetic Analysis Reveals a Wide Distribution and Fusion with Different Catalytic DomainsAnalysis of the phylogenetic distribution of COG1058 members in the three kingdoms of life revealed that they are widely distributed, occurring in approximately half of the eukaryotic, bacterial, and archaeal genomes (Figure 6). The COG1058 domain can be found either as a stand-alone domain, or in a fused form with NMN deamidase or FAD synthase (that catalyzes FMN adenylylation to FAD). In particular, in archaea, in a- and some d-proteobacteria, the COG1058 domain occurs only as a single domain, while in remaining bacterial taxonomic groups it is mostly found fused with PncC (Figure 6A ). Eukaryotes have both single- and two-domain proteins, the latter being composed of the COG1058 domain fused to FAD synthase (Figure 6B). While the single-domain form is mostly present in fungi, the fused form is widely distributed among plants and animals. Notably, in plants the COG1058 domain is located at the N-terminus, whereas in animals it occurs at the C-terminus. The large-scaletopology of the COG1058 phylogenetic tree (Figure 7, and Figure S1) is largely consistent with.
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