Cancer-Associated Isocitrate Dehydrogenase Mutation: Structural Basis of Enzyme Inactivation
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Date
2014-01-09
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Johns Hopkins University
Abstract
Isocitrate dehydrogenase enzymes catalyze the oxidative decarboxylation of isocitrate to α-ketoglutarate. Somatic point mutations in the IDH1 gene are observed in glioblastoma multiforme and acute myeloid leukemia, with a hot spot identified at amino acid residue R132. These mutant enzymes display neomorphic activity such that enzymes with this mutation now catalyze the reduction of α-ketoglutarate to 2-hydroxyglutarate. Given their tumorigenic potential, mutant IDH1 enzymes are an attractive drug target for cancer therapies since they possess a cancer specific mutation and produce a metabolite that can be used as biomarker.
The structure of IDH1 R132H-α-ketoglutarate-NADP was determined to a resolution of 2.1 Å by x-ray crystallography, and demonstrates that the enzyme is an asymmetric homodimer. To determine the binding site of the small molecules A07 and ZAG within IDH1 R132H, we determined the structure of IDH1 R132H-isocitrate-NADP-A07 with data to 3.0 Å and that of IDH1 R132H-isocitrate-NADP-ZAG to 3.3 Å. In both structures, the small molecules bind at an allosteric site at the dimer interface of the semi-open conformation of IDH1 R132H. The allosteric site locks the enzyme in a conformation that prevents the formation of the pre-transition state necessary for the enzyme to undergo catalysis. This work shows that the dimer interface of IDH1 has a pre-defined pocket that participates in catalysis as it transitions between the open and closed conformations. The temperature factor of the binding site area is higher than that of the other portions of the structure, suggesting that this protein-protein interface participates in the conformational changes required for catalysis.
This work shows that the preformed cavity allows for binding of IDH1 to allosteric inhibitors. Using a combination of high throughput screening, inhibition assays, and structural biology, we identified a protein-protein interface that provides another opportunity for structure-based drug design
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Keywords
isocitrate dehydrogenase, cancer, gain-of-function, 2-hydroxyglutarate, somatic mutation