Isocitrate dehydrogenase

Overview:Overview:

Isocitrate Dehydrogenase is an enzyme that is used during the third step of the citric acid cycle. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme NAD+ is converted to an NADH. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle.

Structure:Structure:

Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.In human isocitrate dehydrogenase there are 4 subunits.

Template:STRUCTURE 1t0l

The Active SiteThe Active Site

The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mn+ or Ca2+. This metal ion seems to be essential for catalysis. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine. Across species these are not perfectly conserved by they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands.

The blue is the Mn+ ion next to the ligand which is surrounded by the residuals of that active site.

FunctionFunction

Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form. Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme .

MechanismMechanism

The mechanism described is for porcine isocitrate dehydrogenase because is is better understood than the human mechanism. The alcohol group off the alpha-carbon is deprotonated by the Tyr residue. The electrons pust to the oxygen atom to form a double bond (keytone). The remaining alpha carbon hydrogen is removed using NAD+/NADP+ as an electron accepting cofactor. A carboxyl group pushes electrons down so an oxygen steals a nearby proton off a Lysine amino acid. The Tyr deprotanates the carboxylic acid resulting in electron pushing that ejects a CO2. The two negatively charged oxygen's on the other side of the molecule are stabilized by the Mn2+. The double bond that was formed between the alpha and beta carbon removes a proton from the Tyr residue and the oxygen returns the a keytone and the alpha-ketoglutarate is formed. This is illustrated in the figure below.

The mechanism by which isocitrate is converted to alpha-ketoglutarate