Isocitrate dehydrogenase

Isocitrate dehydrogenase (IDH) (EC 1.1.1.42) and (EC 1.1.1.41) 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

The NAD-IDH is composed of three subunits, is allosterically regulated, and requires an integrated Mg2+ or Mn2+ ion. The closest homologue that has a known structure is the E. coli NADP-dependent IDH, which has only two subunits and a 13% identity and 29% similarity based on the amino acid sequences, making it dissimilar to human IDH and not suitable for close comparison. All the known NADP-IDHs are homodimers. Most isocitrate dehydrogenases are dimers, to be specific, homodimers (two identical monomer subunits forming one dimeric unit). In comparing C. glutamicum and E. coli, monomer and dimer, respectively, both enzymes were found to "efficiently catalyze identical reactions." However, C. glutamicum was recorded as having ten times as much activity than E. coli and seven times more affinitive/specific for NADP. C. glutamicum favored NADP+ over NAD+. In terms of stability with response to temperature, both enzymes had a similar Tm or melting temperature at about 55 °C to 60 °C. However, the monomer C. glutamicum showed a more consistent stability at higher temperatures, which was expected. The dimer E. coli showed stability at a higher temperature than normal due to the interactions between the two monomeric subunits. The structure of Mycobacterium tuberculosis (Mtb) ICDH-1 bound with NADPH and Mn(2+) bound has been solved by X-ray crystallography. It is a homodimer in which each subunit has a Rossmann fold, and a common top domain of interlocking β sheets. Mtb ICDH-1 is most structurally similar to the R132H mutant human ICDH found in CNS WHO grade 4 astrocytomas, formerly classified as 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.

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+. Water molecules help to deprotonate the oxygen atoms of isocitrate. The second box in the figure illustrates step 1 of the reaction, which is the oxidation of the alpha-carbon (C2 here, also called alpha-C). In this process, the alcohol group of the alpha-carbon is deprotonated and the resulting lone pair of electrons forms a ketone group on that carbon. NAD+/NADP+ acts as an electron-accepting cofactor and collects the resulting hydride from C2. The oxidation of the alpha carbon introduces a molecular arrangement where electrons (in the next step) will flow from the nearby carboxyl group and push the electrons of the double bonded oxygen up onto the oxygen atom itself, which collects a proton from a nearby lysine. The third box illustrates step 2, which is the decarboxylation of oxalosuccinate. In this step, the carboxyl group oxygen is deprotonated by a nearby tyrosine, and those electrons flow down to C2. Carbon dioxide, the leaving group, detaches from the beta carbon of isocitrate (C3) and the electrons flow to the ketone oxygen attached to the alpha carbon, granting a negative charge to the associated oxygen atom and forming an alpha-beta unsaturated double bond between carbons 2 and 3. The fourth and final box illustrates step 3, which is the saturation of the alpha-beta unsaturated double bond that formed in the previous step. The negatively charged oxygen (attached to the alpha-carbon) donates its electrons, reforming the ketone double bond and pushing another lone pair (the one that forms the double bond between the alpha and beta carbons) "off" the molecule. This lone pair, in turn, picks up a proton from the nearby tyrosine. This reaction results in the formation of alpha-ketoglutarate, NADH + H+/NADPH + H+, and CO2.

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