Biochemical and phylogenetic characterization of a monomeric isocitrate dehydrogenase from a marine methanogenic archaeon Methanococcoides methylutens

Biochemical and Phylogenetic Characterization of a Novel NADP+-Specific Isocitrate Dehydrogenase From the Marine Microalga Phaeodactylum tricornutum

“…Interestingly, even though the H 604 L/R 615 D/R 664 S mutant enzyme could utilize NAD + as the coenzyme, the catalytic efficiency was fairly low. Similar results were obtained in other studies that sought to convert the coenzyme dependence of IDH from NADP + to NAD + , such as for M. methylutens IDH (Wang et al, 2020), X. fastidiosa IDH (Lv et al, 2018), and X. campestris IDH (Lv et al, 2016) (Supplementary Table S2). These results indicated that additional amino acid residues are involved in the binding of NAD + by monomeric IDHs, and further imply that the mechanisms involved in NAD + catalysis are more complex than those involved in NADP + catalysis in the type III IDH subfamily.…”

“…Recombinant PtIDH2 retained more than 60% activity across a wide pH range (7.5-9.0) (Figure 4A). The optimum pH value for PtIDH2 was approximately 8.0 regardless of whether Mn 2+ or Mg 2+ was used, similar to that observed for the bacterial monomeric NADP-IDHs from Methanococcoides methylutens (pH 8.2 with Mn 2+ and 8.5 with Mg 2+ ) and Streptomyces lividans (pH 8.5 with Mn 2+ ) (Zhang et al, 2009;Wang et al, 2020), but lower than that for Streptomyces avermitilis IDH (pH 9.4 with Mn 2+ ) and C. glutamicum IDH (pH 9.0 with Mg 2+ ) (Chen and Yang, 2000;Wang et al, 2011) and higher than that for X. fastidiosa IDH (pH 7.75 with Mn 2+ ) (Lv et al, 2018).…”

“…Additionally, two types of IDHs—monomeric and homodimeric NADP-IDHs—can be distinguished in the type III subfamily based on coenzyme specificity and oligomeric state ( Wang et al, 2015 ; Wang et al, 2018 ). All type III IDHs reported to date are derived from prokaryotes, including both bacteria and archaea ( Wang et al, 2020 ). In this study, a novel type III homotetrameric NADP-IDH from the marine alga P. tricornutum , a eukaryote, was characterized in detail for the first time.…”

“…IDHs are widely distributed in all living organisms, including archaea, bacteria, and eukaryotes. However, to date, type III IDHs, such as Azotobacter vinelandii IDH (AvIDH), Corynebacterium glutamicum IDH (CgIDH), Campylobacter concisus IDH ( Wang et al, 2019 ), and Methanococcoides methylutens IDH (MmIDH) ( Wang et al, 2020 ), have been identified only in prokaryotes. Over recent years, with the development of high-throughput genome sequencing technology, a large number of complete genome sequences from marine organisms have become available.…”

Enzymatic Characterization of the Isocitrate Dehydrogenase with Dual Coenzyme Specificity from the Marine Bacterium Umbonibacter marinipuiceus

“…Subsequently, certain bacteria encountered environmental stress due to carbon source limitations, leading to a coenzyme specificity shift in IDH from NAD + to NADP + , and this transition provided the bacteria with the necessary reducing power, NADPH. The coenzyme adaptive evolution mechanism of IDH has been reproduced and validated in E. coli [10,13,30,31], and numerous experiments have demonstrated its applicability across different subfamilies [21,[32][33][34][35]. The majority of the existing NAD-IDHs are found in the Type I subfamily, while a small number are also present in the Type II and Type III subfamilies.…”