3MAS: Crystal structure of heterodimeric R132H mutant of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP and isocitrate

Citation:
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 alpha-ketoglutarate (alphaKG) 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 alphaKG reduction activity and propose that Tyr139 may play a vital role by compensating the increased negative charge on the C2 atom of alphaKG during the transfer of a hydride anion from NADPH to alphaKG, which provides new insights into the mechanism of the "on switch" of the hypothetically oncogenic reduction activity of IDH1 by this mutation.
PDB ID: 3MASDownload
MMDB ID: 86094
PDB Deposition Date: 2010/3/24
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 3.2  Å
Source Organism:
Similar Structures:
Biological Unit for 3MAS: dimeric; determined by author and by software (PISA)
Molecular Components in 3MAS
Label Count Molecule
Proteins (2 molecules)
1
Isocitrate Dehydrogenase [nadp] Cytoplasmic(Gene symbol: IDH1)
Molecule annotation
1
Isocitrate Dehydrogenase [nadp] Cytoplasmic(Gene symbol: IDH1)
Molecule annotation
Chemicals (4 molecules)
1
2
2
2
* Click molecule labels to explore molecular sequence information.

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