8BAY

Crystal Structure of IDH1 variant R132C S280F in complex with NADPH, Ca2+ and 3-butyl-2-oxoglutarate

Summary for 8BAY

• Entry DOI: 10.2210/pdb8bay/pdb
• Related: 7PJM 7PJN
• Descriptor: Isocitrate dehydrogenase [NADP] cytoplasmic, GLYCEROL, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, ... (7 entities in total)
• Functional Keywords: oxidoreductase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 3
• Total formula weight: 147422.41

Authors

Rabe, P.,Schofield, C.J.,Reinbold, R.,Brewitz, L. (deposition date: 2022-10-12, release date: 2022-11-02, Last modification date: 2024-02-07)

Primary citation

Liu, X.,Reinbold, R.,Liu, S.,Herold, R.A.,Rabe, P.,Duclos, S.,Yadav, R.B.,Abboud, M.I.,Thieffine, S.,Armstrong, F.A.,Brewitz, L.,Schofield, C.J.
Natural and synthetic 2-oxoglutarate derivatives are substrates for oncogenic variants of human isocitrate dehydrogenase 1 and 2.
J.Biol.Chem., 299:102873-102873, 2023

PubMed Abstract: Variants of isocitrate dehydrogenase (IDH) 1 and 2 (IDH1/2) alter metabolism in cancer cells by catalyzing the NADPH-dependent reduction of 2-oxoglutarate (2OG) to (2R)-hydroxyglutarate. However, it is unclear how derivatives of 2OG can affect cancer cell metabolism. Here, we used synthetic C3- and C4-alkylated 2OG derivatives to investigate the substrate selectivities of the most common cancer-associated IDH1 variant (R132H IDH1), of two cancer-associated IDH2 variants (R172K IDH2, R140Q IDH2), and of WT IDH1/2. Absorbance-based, NMR, and electrochemical assays were employed to monitor WT IDH1/2 and IDH1/2 variant-catalyzed 2OG derivative turnover in the presence and absence of 2OG. Our results reveal that 2OG derivatives can serve as substrates of the investigated IDH1/2 variants, but not of WT IDH1/2, and have the potential to act as 2OG-competitive inhibitors. Kinetic parameters reveal that some 2OG derivatives, including the natural product 3-methyl-2OG, are equally or even more efficient IDH1/2 variant substrates than 2OG. Furthermore, NMR and mass spectrometry studies confirmed IDH1/2 variant-catalyzed production of alcohols in the cases of the 3-methyl-, 3-butyl-, and 3-benzyl-substituted 2OG derivatives; a crystal structure of 3-butyl-2OG with an IDH1 variant (R132C/S280F IDH1) reveals active site binding. The combined results highlight the potential for (i) IDH1/2 variant-catalyzed reduction of 2-oxoacids other than 2OG in cells, (ii) modulation of IDH1/2 variant activity by 2-oxoacid natural products, including some present in common foods, (iii) inhibition of IDH1/2 variants via active site binding rather than the established allosteric mode of inhibition, and (iv) possible use of IDH1/2 variants as biocatalysts.

PubMed: 36621625
DOI: 10.1016/j.jbc.2023.102873

Experimental method

X-RAY DIFFRACTION (2.35 Å)