Isocitrate dehydrogenase

Isocitrate dehydrogenase (IDH) () and () is an enzyme that catalyzes the oxidative decarboxylation of isocitrate, producing alpha-ketoglutarate (α-ketoglutarate) and CO₂. This is a two-step process, which involves oxidation of isocitrate (a secondary alcohol) to oxalosuccinate (a ketone), followed by the decarboxylation of the carboxyl group beta to the ketone, forming alpha-ketoglutarate. In humans, IDH exists in three isoforms: IDH3 catalyzes the third step of the citric acid cycle while converting NAD⁺ to NADH in the mitochondria. The isoforms IDH1 and IDH2 catalyze the same reaction outside the context of the citric acid cycle and use NADP⁺ as a cofactor instead of NAD⁺. They localize to the cytosol as well as the mitochondrion and peroxisome.

Structure

thumb|right|300px|One active site on the Porcine NADP⁺ dependent enzyme (green). as [[Glioblastoma|glioblastomas. Similar to human R132H ICDH, Mtb ICDH-1 also catalyzes the formation of α-hydroxyglutarate.

Regulation

The IDH step of the citric acid cycle is often (but not always) an irreversible reaction due to its large negative change in free energy. It must therefore be carefully regulated to avoid depletion of isocitrate (and therefore an accumulation of alpha-ketoglutarate). The reaction is stimulated by the simple mechanisms of substrate availability (isocitrate, NAD⁺ or NADP⁺, Mg²⁺ / Mn²⁺ ), product inhibition by NADH (or NADPH outside the citric acid cycle) and alpha-ketoglutarate, and competitive feedback inhibition by ATP. A conserved ncRNA upstream of the icd gene which codes for NADP⁺-dependent isocitrate dehydrogenase (IDH) has been reported in bacterial genomes, due to its characteristics this ncRNA resembles previous regulatory motifs called riboswitches, icd-II ncRNA motif has been proposed as a strong candidate riboswitch.

Catalytic mechanisms

Isocitrate dehydrogenase catalyzes the chemical reactions:

and the same reaction where the oxidizing agent is NADP⁺ instead of NAD⁺.

The overall free energy for this reaction is -8.4 kJ/mol.

thumb|Catalytic mechanism of the breakdown of isocitrate into oxalosuccinate, then into a final product of alpha-ketuglutarate. The oxalosuccinate intermediate is hypothetical; it has never been observed in the decarboxylating version of the enzyme.

Steps

Within the citric acid cycle, isocitrate, produced from the isomerization of citrate, undergoes both oxidation and decarboxylation. The enzyme isocitrate dehydrogenase (IDH) holds isocitrate within its active site using the surrounding amino acids, including arginine, tyrosine, asparagine, serine, threonine, and aspartic acid.

In the provided figure, the first box shows the overall isocitrate dehydrogenase reaction. The necessary reactants for this enzyme mechanism are isocitrate, NAD⁺/NADP⁺, and Mn²⁺ or Mg²⁺. The products of the reaction are alpha-ketoglutarate, carbon dioxide, and NADH + H⁺/NADPH + H⁺. This reaction results in the formation of alpha-ketoglutarate, NADH + H⁺/NADPH + H⁺, and CO₂.

Detailed mechanism

Two aspartate amino acid residues (below left) are interacting with two adjacent water molecules (w6 and w8) in the Mn²⁺ isocitrate porcine IDH complex to deprotonate the alcohol off the alpha-carbon atom. The oxidation of the alpha-C also takes place in this picture where NAD⁺ accepts a hydride resulting in oxalosuccinate. Along with the sp³ to sp² stereochemical change around the alpha-C, there is a ketone group that is formed from the alcohol group. The formation of this ketone double bond allows for resonance to take place as electrons coming down from the leaving carboxylate group move towards the ketone.

The decarboxylation of oxalosuccinate (below center) is a key step in the formation of alpha-ketoglutarate. In this reaction, the lone pair on the adjacent Tyrosine hydroxyl abstracts the proton off the carboxyl group.

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| thumb|300px|Oxidoreductase step where NAD⁺ is used to accept a hydride.

| thumb|left|375px|Porcine Mitochondrial NADP⁺-dependent Isocitrate Dehydrogenase Complexed with Mn²⁺ and Isocitrate.Specific mutations in the isocitrate dehydrogenase gene IDH1 have been found in several tumor types, notably brain tumors including astrocytoma and oligodendroglioma. Furthermore, mutations of IDH2 and IDH1 were found in up to 20% of cytogenetically normal acute myeloid leukemia (AML). These mutations are known to produce D-2-hydroxyglutarate from alpha-ketoglutarate. D-2-hydroxyglutarate accumulates to very high concentrations which inhibits the function of enzymes that are dependent on alpha-ketoglutarate. This leads to a hypermethylated state of DNA and histones, which results in different gene expression that can activate oncogenes and inactivate tumor-suppressor genes. Ultimately, this may lead to the types of cancer described above. Somatic mosaic mutations of this gene have also been found associated to Ollier disease and Maffucci syndrome. However, recent studies have also shown that D-2-hydroxyglutarate may be converted back into alpha-ketoglutarate either enzymatically or non-enzymatically. Further studies are required to fully understand the roles of IDH1 mutation (and D-2-hydroxyglutarate) in cancer. Recent research highlighted cancer-causing mutations in isocitrate dehydrogenase which may cause accumulation of the metabolite D-2-hydroxyglutarate (D-2HG). Notarangelo et al. showed that such high concentrations of D-2HG could act as a direct inhibitor of lactate dehydrogenase in mouse T cells. Inhibition of this metabolic enzyme altered glucose metabolism in the T cells and inhibited their proliferation, cytokine production, and ability to kill target cells.

Isozymes

The following is a list of human isocitrate dehydrogenase isozymes:

NADP⁺ dependent

Each NADP⁺-dependent isozyme functions as a homodimer:

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NAD⁺ dependent

The isocitrate dehydrogenase 3 isozyme is a heterotetramer that is composed of two alpha subunits, one beta subunit, and one gamma subunit:

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See also

• Oxidoreductase
• Myelodysplastic syndrome#IDH1 and IDH2 mutations
• Oncometabolism
• Isocitrate/isopropylmalate dehydrogenase family

References

External links

• Isocitrate dehydrogenase: RCSB PDB Molecule of the Month