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Isocitrate dehydrogenase (EC 1.1.1.42), also known as IDH, is an enzyme which participates in the citric acid cycle. It catalyzes the third step of the cycle: the oxidative decarboxylation of isocitrate, producing alpha-ketoglutarate (α-ketoglutarate) and CO₂ while converting NAD⁺ to NADH. 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. Another isoform of the enzyme catalyzes the same reaction, however this reaction is unrelated to the citric acid cycle, is carried out in the cytosol as well as the mitochondrion, and uses NADP⁺ as a cofactor instead of NAD⁺. Image File history File links Question_book-3. ... The Entrez logo The Entrez Global Query Cross-Database Search System allows access to databases at the National Center for Biotechnology Information (NCBI) website. ... Look up Hugo in Wiktionary, the free dictionary. ... The Mendelian Inheritance in Man project is a database that catalogues all the known diseases with a genetic component, and - when possible - links them to the relevant genes in the human genome. ... National Center for Biotechnology Information logo The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health. ... Swiss-Prot is a curated biological database of protein sequences created in 1986 by Amos Bairoch during his PhD and developed by the Swiss Institute of Bioinformatics and the European Bioinformatics Institute. ... The Enzyme Commission number (EC number) is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze. ... Short and long arms Chromosome. ... Chromosome 2 is one of the 23 pairs of chromosomes in humans. ... The Enzyme Commission number (EC number) is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze. ... Ribbon diagram of the enzyme TIM, surrounded by the space-filling model of the protein. ... Overview of the citric acid cycle The citric acid cycle (also known as the tricarboxylic acid cycle, the TCA cycle, or the Krebs cycle, after Hans Adolf Krebs who identified the cycle) is a series of chemical reactions of central importance in all living cells that use oxygen as part... Isocitrate is a substrate of the citric acid cycle. ... Ketoglutaric acid is used for either of two crystalline keto derivatives C5H6O5 of glutaric acid. ... Carbon dioxide is a chemical compound composed of two oxygen atoms covalently bonded to a single carbon atom. ... Nicotinamide adenine dinucleotide (NAD+ or in older notation DPN+) is an important coenzyme found in cells. ... Nicotinamide adenine dinucleotide (NAD+ or in older notation DPN+) is an important coenzyme found in cells. ... Isocitrate is a substrate of the citric acid cycle. ... This article does not cite any references or sources. ... Oxalosuccinate is a substrate of the citric acid cycle. ... Ketone group A ketone (pronounced as key tone) is either the functional group characterized by a carbonyl group (O=C) linked to two other carbon atoms or a chemical compound that contains this functional group. ... Electron micrograph of a mitochondrion showing its mitochondrial matrix and membranes In cell biology, a mitochondrion (plural mitochondria) is a membrane-enclosed organelle that is found in most eukaryotic cells. ... Nicotinamide adenine dinucleotide (NAD+ or in older notation DPN+) is an important coenzyme found in cells. ...

The CAS number for this type of the enzyme is [9028-48-2]. CAS registry numbers are unique numerical identifiers for chemical compounds, polymers, biological sequences and alloys. ...

Energetics:

The overall free energy for this reaction with either isoform is -8.4 kJ/mol. IDH lowers the K_m (Michaelis constant) of isocitrate without lowering the V_max (maximum reaction rate - see Michaelis constant for more details). Michaelis-Menten kinetics describe the rate of enzyme mediated reactions for many enzymes. ... Michaelis-Menten kinetics describe the rate of enzyme mediated reactions for many enzymes. ...

Structure:

The NAD-IDH is composed of 3 subunits, is allosterically regulated, and requires an integrated Mg²⁺ or Mn²⁺ ion. The closest homologue which has a known structure is the E. coli NADP-dependent IDH, which only has 2 subunits and a 13% identity and 29% similarity based on the amino acid sequences, making it a far cry from human IDH and not suitable for close comparison. All the known NADP-IDHs are homodimers. See also Entamoeba coli. ...

Regulation:

The IDH step of the citric acid cycle, due to its large negative free energy change, is one of the irreversible reactions in the citric acid cycle and therefore must be carefully regulated to avoid unnecessary depletion of isocitrate (and therefore an accumulation of alpha-ketoglutarate). The reaction is stimulated by the simple mechanisms of substrate availability (isocitrate, NAD⁺, Mg²⁺ / Ca²⁺ ), product inhibition (by NADH and alpha-ketoglutarate), and competitive feedback inhibition (by ATP). Nicotinamide adenine dinucleotide (NAD+ or in older notation DPN+) is an important coenzyme found in cells. ... Nicotinamide adenine dinucleotide (NAD+) Nicotinamide adenine dinucleotide (NAD) and nicotinamide adenine dinucleotide phosphate (NADP) are two important coenzymes found in cells. ... Adenosine 5-triphosphate (ATP) is a multifunctional nucleotide that is most important as a molecular currency of intracellular energy transfer. ...

Catalytic Mechanism:

Catalytic mechanism of the breakdown of isocitrate into oxalosuccinate, then into a final product of alpha-ketuglutarate

Image File history File links No higher resolution available. ... Image File history File links No higher resolution available. ...

Steps Broken Down:

Within the citric acid cycle, isocitrate, produced from the isomerization of citrate, undergoes both oxidation and decarboxylation. Using the enzyme Isocitrate Dehydrogenase (IDH), isocitrate is held within its active site by surrounding Arginine, Tyrosine, Asparagine, Serine, Threonine, and Aspartic Acid residues. The first box shows the overall isocitrate dehydrogenase reaction. The reactants necessary for this enzyme mechanism to work 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 are used to help deprotonate the oxygens (O3) of isocitrate.

The second box is Step 1 which is the oxidation of the alpha-C (C#2). Oxidation is the first step that isocitrate goes through. In this process, the alchohol group off the alpha-carbon (C#2) is deprotonated and the electrons flow to the alpha-C forming a ketone group and removing a hydride off C#2 using NAD+/NADP+ as an electron accepting cofactor. The oxidation of the alpha-C allows for a position where electrons (in the next step) will be coming down from the carboxylate group and pushing the electrons (making the double bonded oxygen) back up on the oxygen or grabbing a nearby proton off a nearby Lysine amino acid.

The third box is Step 2 which is the decarboxylation of oxalosuccinate. In this step, the carboxylate group oxygen is deprotonated by a nearby Tyrosine amino acid and those electrons flow down to carbon 2. Carbon dioxide leaves the beta-C of isocitrate as a leaving group with the electrons flowing to the ketone oxygen off the alpha-C placing a negative charge on the oxygen of the alpha-C and forming an alpha-beta unsaturated double bond between carbons 2 and 3. The lone pair on the alpha-C oxygen picks up a proton from a nearby Lysine amino acid.

The fourth box is Step 3 which is the saturation of the alpha-beta unsaturated double bond between carbons 2 and 3. In this step of the reaction, Lysine deprotonates the oxygen off the alpha carbon and the lone pair of electrons on the oxygen of the alpha carbon comes down reforming the ketone double bond and pushing the lone pair (forming the double bond between the alpha and beta carbon) off, picking up a proton from the nearby Tyrosine amino acid. This reaction results in the formation of alpha-ketoglutarate, NADH+H+/NADPH+H+, and CO₂.

3-D structure Mechanism:

Oxidoreductase step where NAD+ is used to accept a hydride.

Looking at the 3-D structures to the left, two Aspartate amino acids 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. 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 form 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. Image File history File links No higher resolution available. ... Image File history File links No higher resolution available. ...

Decarboxylation of oxalosuccinate. From Template:J. Mol. Biol (2007) 372, 130-149.

The decarboxylation of oxalosuccinate is a key step in the formation of alpha-ketoglutarate. In this reaction, the lone pair on the adjacent Tyrosine oxygen pulls off the proton of the carboxyl group. This carboxyl group is also referred to as the beta subunit of isocitrate. The deprotonation of the carboxyl proton causes the lone pair of electrons to move down making carbon dioxide and separating from oxalosuccinate. The electrons continue to move towards the alpha carbon pushing the double bond electrons (making the ketone) up to pull a proton off an adjacent Lysine residue. An alpha-beta unsaturated double bond results between carbon 2 and three. As you can see in the picture, the green ion represents either Mg2+ or Mn2+, which is a cofactor necessary for this reaction to occur. The metal-ion forms a little complex through ionic interactions with the oxygen atoms on the fourth and fifth carbons (also known as the gamma subunit of isocitrate). Image File history File links No higher resolution available. ... Image File history File links No higher resolution available. ...

Saturation of the alpha-beta unsaturated double bond. From Template:J. Mol. Biol (2007) 372, 130-149.

After carbon dioxide leaves oxalosuccinate in the decarboxylation step, the alcohol on carbon 2 will want to reform the ketone double bond because that’s a more stable form than the enol form which it is in. The reformation of the ketone double bond is started by the deprotonation of that oxygen off the alpha carbon (C#2) by the same Lysine that protonated the oxygen in the first place. The lone pair of electrons moves down kicking off the lone pairs that were making the double bond. This lone pair of electrons pulls a proton off the Tyrosine that deprotonated the carboxyl group in the decarboxylation step. The reason that we can say that the Lys and Tyr residues will be the same from the previous step because they are helping in holding the isocitrate molecule in the active site of the enzyme. These two residues will be able to hydrogen bond back and forth as long as they’re close enough to the substrate. Image File history File links No higher resolution available. ... Image File history File links No higher resolution available. ...

alpha-ketoglutarate. From Template:J. Mol. Biol (2007) 372, 130-149.

The isocitrate dehydrogenase enzyme as stated above produces alpha-ketoglutarate, carbon dioxide, and NADH+H+/NADPH+H+. There are three changes that occurred throughout the reaction. The oxidation of Carbon 2, the decarboxylation (loss of carbon dioxide) off Carbon 3, and the formation of a ketone group with a stereochemical change from sp3 to sp2. Image File history File links No higher resolution available. ... Image File history File links No higher resolution available. ...

Porcine Mitochondrial NADP+=dependent Isocitrate Dehydrogenase Complexed with Mn2+ and Isocitrate. From Template:PDB 1LWD.

Right: Surface view of the active site pocket where isocitrate is bounded by polar amino acids. Image File history File links Size of this preview: 800 × 591 pixelsFull resolution‎ (1,162 × 859 pixels, file size: 75 KB, MIME type: image/jpeg)Active site surface view of the pocket where Isocitrate binds to Porcine Mitochondrial enzyme. ... Image File history File links Size of this preview: 800 × 591 pixelsFull resolution‎ (1,162 × 859 pixels, file size: 75 KB, MIME type: image/jpeg)Active site surface view of the pocket where Isocitrate binds to Porcine Mitochondrial enzyme. ...

Porcine Mitochondrial NADP+-dependent Isocitrate Dehydrogenase Complexed with Mn2+ and Isocitrate. From Template:PDB 1LWD.

Porcine Enzyme complex; Active site isocitrate and adjacent A.A. From Template:PDB 1LWD.

Left: The Porcine Heart Mitochondrial Enzyme. In this picture you can see that the enzyme is a homeodimer where it is made up of two identical subunits and therefore two identical active sites. Right: This is the active site bared down to just isocitrate, Mn2+ and the surrounding interactive amino acids. Image File history File links Size of this preview: 800 × 591 pixelsFull resolution‎ (1,162 × 859 pixels, file size: 200 KB, MIME type: image/jpeg) From PDB 1LWD. Created using Chimera Program. ... Image File history File links Size of this preview: 800 × 591 pixelsFull resolution‎ (1,162 × 859 pixels, file size: 200 KB, MIME type: image/jpeg) From PDB 1LWD. Created using Chimera Program. ... Image File history File links Size of this preview: 800 × 591 pixelsFull resolution‎ (1,162 × 859 pixels, file size: 44 KB, MIME type: image/jpeg) From PDB 1LDW. Created using Chimera. ... Image File history File links Size of this preview: 800 × 591 pixelsFull resolution‎ (1,162 × 859 pixels, file size: 44 KB, MIME type: image/jpeg) From PDB 1LDW. Created using Chimera. ...

Porcine IDH complex, Arg AA stabilizing isocitrate in the active site. From Template:PDB 1LWD.

Above: In this picture, residues Arg110, Arg133, and Arg101 are the three main stabilizing amino acids. They help to hold isocitrate in the active site and in the right orientation for isocitrate dehydrogenase to take place. Image File history File links Size of this preview: 800 × 499 pixelsFull resolution‎ (1,135 × 708 pixels, file size: 30 KB, MIME type: image/jpeg) From PDB 1LWD. Created using Chimera. ... Image File history File links Size of this preview: 800 × 499 pixelsFull resolution‎ (1,135 × 708 pixels, file size: 30 KB, MIME type: image/jpeg) From PDB 1LWD. Created using Chimera. ...

One active site on the Porcine NADP+ dependent enzyme (green). From Template:PDB 1LWD.

E.coli with 3 active sites [1 for NADP+(far right)] shown (green). From Template:PDB 1CW7.

Left: Porcine Heart Mitochondrial NADP+-dependent enzyme showing an active spot in green. Porcine enzyme is a homeodimer and has another active site on the other side. Right: Escherichia coli was the first isocitrate dehydrogenase structure derived. There are three active sites. Three isocitrates, one isocitrate in the binding site for NADP+. Image File history File links Size of this preview: 800 × 591 pixelsFull resolution‎ (1,162 × 859 pixels, file size: 129 KB, MIME type: image/jpeg) From PDB 1LWD. Created using Chimera Program. ... Image File history File links Size of this preview: 800 × 591 pixelsFull resolution‎ (1,162 × 859 pixels, file size: 129 KB, MIME type: image/jpeg) From PDB 1LWD. Created using Chimera Program. ... Image File history File links Size of this preview: 800 × 499 pixelsFull resolution‎ (1,135 × 708 pixels, file size: 113 KB, MIME type: image/jpeg) From PDB 1CW7. ... Image File history File links Size of this preview: 800 × 499 pixelsFull resolution‎ (1,135 × 708 pixels, file size: 113 KB, MIME type: image/jpeg) From PDB 1CW7. ...

See also

• Oxidoreductase

In biochemistry, an oxidoreductase is an enzyme that catalyzes the transfer of electrons from one molecule (the oxidant, also called the hydrogen donor or electron donor) to another (the reductant, also called the hydrogen acceptor or electron acceptor). ...

References

• IUBMB entry for 1.1.1.42
• BRENDA references for 1.1.1.42 (Recommended.)
• PubMed references for 1.1.1.42
• PubMed Central references for 1.1.1.42
• Google Scholar references for 1.1.1.42

External links

• IUBMB entry for 1.1.1.42

• KEGG entry for 1.1.1.42

• BRENDA entry for 1.1.1.42

• NiceZyme view of 1.1.1.42

• EC2PDB: PDB structures for 1.1.1.42

• PRIAM entry for 1.1.1.42

• PUMA2 entry for 1.1.1.42

• IntEnz: Integrated Enzyme entry for 1.1.1.42

• MetaCyc entry for 1.1.1.42

• Atomic-resolution structures of enzymes belonging to this class