7E2W

Crystal structure of isocitrate dehydrogenase from Ostreococcus tauri in complex with isocitrate and magnesium(II)

Replaces:  6IXU

Summary for 7E2W

• Entry DOI: 10.2210/pdb7e2w/pdb
• Related: 6IXL 6IXN 6IXT
• Descriptor: Isocitrate dehydrogenase (NAD(+)), mitochondrial, ISOCITRIC ACID, MAGNESIUM ION, ... (7 entities in total)
• Functional Keywords: isocitrate dehydrogenase, oxidoreductase
• Biological source: Ostreococcus tauri
• Total number of polymer chains: 4
• Total formula weight: 188157.06

Authors

Zhu, G.P.,Tang, W.G.,Wang, P. (deposition date: 2021-02-07, release date: 2021-05-19, Last modification date: 2023-11-29)

Primary citation

Tang, W.,Wu, M.,Qin, N.,Liu, L.,Meng, R.,Wang, C.,Wang, P.,Zang, J.,Zhu, G.
Crystal structures of NAD + -linked isocitrate dehydrogenase from the green alga Ostreococcus tauri and its evolutionary relationship with eukaryotic NADP + -linked homologs.
Arch.Biochem.Biophys., 708:108898-108898, 2021

PubMed Abstract: NAD-linked isocitrate dehydrogenases (NAD-IDHs) catalyze the oxidative decarboxylation of isocitrate into α-ketoglutarate. Previously, we identified a novel phylogenetic clade including NAD-IDHs from several algae in the type II subfamily, represented by homodimeric NAD-IDH from Ostreococcus tauri (OtIDH). However, due to its lack of a crystalline structure, the molecular mechanisms of the ligand binding and catalysis of OtIDH are little known. Here, we elucidate four high-resolution crystal structures of OtIDH in a ligand-free and various ligand-bound forms that capture at least three states in the catalytic cycle: open, semi-closed, and fully closed. Our results indicate that OtIDH shows several novel interactions with NAD, unlike type I NAD-IDHs, as well as a strictly conserved substrate binding mode that is similar to other homologs. The central roles of Lys283' in dual coenzyme recognition and Lys234 in catalysis were also revealed. In addition, the crystal structures obtained here also allow us to understand the catalytic mechanism. As expected, structural comparisons reveal that OtIDH has a very high structural similarity to eukaryotic NADP-linked IDHs (NADP-IDHs) within the type II subfamily rather than with the previously reported NAD-IDHs within the type I subfamily. It has also been demonstrated that OtIDH exhibits substantial conformation changes upon ligand binding, similar to eukaryotic NADP-IDHs. These results unambiguously support our hypothesis that OtIDH and OtIDH-like homologs are possible evolutionary ancestors of eukaryotic NADP-IDHs in type II subfamily.

PubMed: 33957092
DOI: 10.1016/j.abb.2021.108898

Experimental method

X-RAY DIFFRACTION (1.8 Å)