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Publication Abstract from PubMed

The marine diatom Phaeodactylum tricornutum originated from a series of secondary symbiotic events and has been used as a model organism for studying diatom biology. A novel type II homodimeric isocitrate dehydrogenase from P. tricornutum (PtIDH1) was expressed, purified, and identified in detail through enzymatic characterization. Kinetic analysis showed that PtIDH1 is NAD(+)-dependent and has no detectable activity with NADP(+). The catalytic efficiency of PtIDH1 for NAD(+) is 0.16 muM(-1).s(-1) and 0.09 muM(-1).s(-1) in the presence of Mn(2+) and Mg(2+), respectively. Unlike other bacterial homodimeric NAD-IDHs, PtIDH1 activity was allosterically regulated by the isocitrate. Furthermore, the dimeric structure of PtIDH1 was determined at 2.8 A resolution, and each subunit was resolved into four domains, similar to the eukaryotic homodimeric NADP-IDH in the type II subfamily. Interestingly, a unique and novel C-terminal EF-hand domain was first defined in PtIDH1. Deletion of this domain disrupted the intact dimeric structure and activity. Mutation of the four Ca(2+)-binding sites in the EF-hand significantly reduced the calcium tolerance of PtIDH1. Thus, we suggest that the EF-hand domain could be involved in the dimerization and Ca(2+)-coordination of PtIDH1. The current report, on the first structure of type II eukaryotic NAD-IDH, provides new information for further investigation of the evolution of the IDH family.

Biochemical Characterization and Crystal Structure of a Novel NAD(+)-Dependent Isocitrate Dehydrogenase from Phaeodactylum tricornutum.,Huang SP, Zhou LC, Wen B, Wang P, Zhu GP Int J Mol Sci. 2020 Aug 18;21(16). pii: ijms21165915. doi: 10.3390/ijms21165915. PMID:32824636^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.