Structures of Human Cytosolic NADP-dependent Isocitrate Dehydrogenase Reveal a Novel Self-regulatory Mechanism of Activity

Molecular mechanisms of “off-on switch” of activities of human IDH1 by tumor-associated mutation R132H

“…Each IDH1 subunit consists of three domains: a large domain (residues 1-103 and 286-414), a small domain (residues 104-136 and 186-285), and a clasp domain (residues 137-185; Figure 1A). In the structure of the IDH1 H/H -NADP complex, there is an NADP bound at the NADP-binding site of each subunit even though no NADP was added in the crystallization solution, indicating that similar to the wild-type IDH1 [14], the mutant IDH1 was co-purified with a tightly bound NADP from the expression system. In the structures of both IDH1 H/H -NADP-ICT and IDH1 R/H -NADP-ICT complexes, in each subunit, there is an NADP bound at the NADP-binding site and an ICT bound at a site composed of NADP and residues Thr77, Ser94, and Arg100 of the large domain ( Figure 1A and 1B) which is distinct from the ICTbinding site in the IDH1 R/R -NADP-ICT-Ca complex [14] (see discussion later).…”

“…In the structure of the IDH1 H/H -NADP complex, there is an NADP bound at the NADP-binding site of each subunit even though no NADP was added in the crystallization solution, indicating that similar to the wild-type IDH1 [14], the mutant IDH1 was co-purified with a tightly bound NADP from the expression system. In the structures of both IDH1 H/H -NADP-ICT and IDH1 R/H -NADP-ICT complexes, in each subunit, there is an NADP bound at the NADP-binding site and an ICT bound at a site composed of NADP and residues Thr77, Ser94, and Arg100 of the large domain ( Figure 1A and 1B) which is distinct from the ICTbinding site in the IDH1 R/R -NADP-ICT-Ca complex [14] (see discussion later). In all the mutant IDH1 complexes, two key structural elements encompassing residues 132-141 and residues 271-286 (designated as seg1 and seg2, respectively) exhibit great flexibility with the majority of them being disordered (Supplementary information, Table S1; see discussion later).…”

“…In the IDH1 R/R -NADP-ICT-Ca quaternary complex, Arg132, which is strictly conserved in all NADP-dependent IDHs (NADPIDHs) [15], interacts with ICT [14], providing an explanation for the substantially decreased K m (ICT) values of the tumor-derived mutants [12]. Besides the decreased K m , these mutants also show decreased V max [12] or k cat [13] for ICT dehydrogenation and more surprisingly acquire a new function of αKG reduction [13], leading us to speculate that Arg132 may play other functional roles in addition to ICT binding in the catalysis.…”

“…Previously, we have determined the crystal structures of the wild-type dimeric IDH1 (IDH1 R/R ) in complexes with NADP and with NADP, ICT, and Ca 2+ , and showed that the assembly of the active site is a complicated process involving concerted inter-domain motion and conformational changes of two subunits in a cooperative manner and that the enzyme may employ a self-regulatory mechanism to regulate its activity [14]. In the IDH1 R/R -NADP-ICT-Ca quaternary complex, Arg132, which is strictly conserved in all NADP-dependent IDHs (NADPIDHs) [15], interacts with ICT [14], providing an explanation for the substantially decreased K m (ICT) values of the tumor-derived mutants [12].…”

Mitochondrial metabolic remodeling in response to genetic and environmental perturbations

“…Mutations in IDH2 in gliomas occur at a much lower frequency (0–6%) than IDH1 88 in the paralogous amino acid residue—R140—but also at R172. These residues are key in the activity of IDH enzymes: Arg132 and Arg172 in IDH1 and Arg140 and Arg172 in IDH2 form hydrophilic hydrogen bonds with the α‐carboxyl and β‐carboxyl groups of isocitrate to facilitate isocitrate binding in the enzyme active site 99, 100. Mutations in these residues decrease binding affinity for isocitrate and increase binding affinity for NADPH, leading to the reduction of αKG by NADPH and the release of the (R) enantiomer of 2‐hydroxyglutarate [(R)‐2HG] 101.…”