3MAR

Crystal structure of homodimeric R132H mutant of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP

Summary for 3MAR

• Entry DOI: 10.2210/pdb3mar/pdb
• Related: 3MAP 3MAS
• Descriptor: Isocitrate dehydrogenase [NADP] cytoplasmic, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (2 entities in total)
• Functional Keywords: isocitrate dehydrogenase, nicotinamide adenine dinucleotide phosphate, rossmann fold, oxidoreductase
• Biological source: Homo sapiens (human)
• Cellular location: Cytoplasm: O75874
• Total number of polymer chains: 2
• Total formula weight: 97031.44

Authors

Yang, B.,Peng, Y.,Ding, J. (deposition date: 2010-03-24, release date: 2010-11-10, Last modification date: 2023-11-01)

Primary citation

Yang, B.,Zhong, C.,Peng, Y.,Lai, Z.,Ding, J.
Molecular mechanisms of "off-on switch" of activities of human IDH1 by tumor-associated mutation R132H.
Cell Res., 20:1188-1200, 2010

PubMed Abstract: Human cytosolic NADP-IDH (IDH1) has recently been found to be involved in tumorigenesis. Notably, the tumor-derived IDH1 mutations identified so far mainly occur at Arg132, and mutation R132H is the most prevalent one. This mutation impairs the oxidative IDH activity of the enzyme, but renders a new reduction function of converting α-ketoglutarate (αKG) to 2-hydroxyglutarate. Here, we report the structures of the R132H mutant IDH1 with and without isocitrate (ICT) bound. The structural data together with mutagenesis and biochemical data reveal a previously undefined initial ICT-binding state and demonstrate that IDH activity requires a conformational change to a closed pre-transition state. Arg132 plays multiple functional roles in the catalytic reaction; in particular, the R132H mutation hinders the conformational changes from the initial ICT-binding state to the pre-transition state, leading to the impairment of the IDH activity. Our results describe for the first time that there is an intermediate conformation that corresponds to an initial ICT-binding state and that the R132H mutation can trap the enzyme in this conformation, therefore shedding light on the molecular mechanism of the "off switch" of the potentially tumor-suppressive IDH activity. Furthermore, we proved the necessity of Tyr139 for the gained αKG reduction activity and propose that Tyr139 may play a vital role by compensating the increased negative charge on the C2 atom of αKG during the transfer of a hydride anion from NADPH to αKG, which provides new insights into the mechanism of the "on switch" of the hypothetically oncogenic reduction activity of IDH1 by this mutation.

PubMed: 20975740
DOI: 10.1038/cr.2010.145

Experimental method

X-RAY DIFFRACTION (3.41 Å)