Isocitrate Dehydrogenase

Atomic structures have revealed the catalytic steps of a citric acid cycle enzyme

Isocitrate dehydrogenase from yeast (top) and bacteria (bottom).
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Sugar tastes great. This should be no surprise, though, since glucose is the central fuel used by oxygen-breathing organisms. Sugar is broken down in the central catabolic pathways of glycolysis and the citric acid cycle, and ultimately used to construct ATP. The enzymes in these pathways systematically break down glucose molecules into their component parts, capturing the energy of disassembly at each step. Isocitrate dehydrogenase performs the third reaction in the citric acid cycle, which releases one of the carbon atoms as carbon dioxide. In the process, two hydrogens are also removed. One of these, in the form of a hydride, is transferred to the carrier NAD (or NADP), and will be used later to power the rotation of ATP synthase.

Different Approaches to the Same Task

In our cells, this complicated reaction is performed by a complex enzyme, composed of eight chains (the yeast enzyme is shown at the top from PDB entry 3blw ). Four catalytic chains (colored turquoise here) perform the reaction, and four regulatory chains (colored dark blue here) turn the enzyme on and off based on the levels of ATP and ADP in our cells. Bacteria take a simpler approach. They build a smaller enzyme composed of two identical chains, forming two identical active sites (PDB entry 9icd , shown at the bottom). Our cells also build a small version of isocitrate dehydrogenase, which performs this same reaction in the cell cytoplasm, intercoverting isocitrate and alpha-ketoglutarate when they are needed for synthetic tasks.

Control by Phosphorylation

Isocitrate dehydrogenase kinase/phosphatase (orange) bound to isocitrate dehydrogenase.
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The bacterial isocitrate dehydrogenase is not controlled by the levels of ATP and ADP the way our mitochondrial enzyme is, but bacteria still need to be able to turn their enzyme off when there is enough ATP. Bacteria regulate their isocitrate dehydrogenases by adding a phosphate to the protein chain, which blocks the reaction. The enzyme isocitrate dehydrogenase kinase/phosphatase (PDB entry 3lcb , shown here in orange) performs both reactions: adding a phosphate to turn off the enzyme and removing it to activate the enzyme. It decides which reaction is appropriate based on the level of AMP in the cell: when levels are high, AMP binds to a regulatory site, activating the phosphate-removing machinery, otherwise it is active as a phosphate-adding kinase.

Exploring the Structure

Crystallographers have examined many steps in the reaction performed by isocitrate dehydrogenase. The first structures studied the complex of the enzyme with each of its separate substrates and products: isocitrate and magnesium (8icd ), NADP (9icd ), and alpha-ketoglutarate (1ika ), as well as the apo enzyme (3icd ), and the inactive phosphorylated enzyme (4icd ). To examine the details of the reaction itself, however, special experimental techniques were used. By carefully synchronizing the addition of substrates to mutant forms of the enzyme, and then using Laue diffraction to gather crystallographic data in milliseconds, researchers were able observe the unstable intermediates in the reaction. For instance, the Y160F mutant slows down the first step of the reaction (1ide ), so the structure shows the bound complex of isocitrate, NADP and magnesium, caught before they have a chance to react. The K230M mutant slows down the second step, revealing the structure of the intermediate oxalosuccinate before it loses the carbon dioxide (1idc ). Click on the image to see an interactive Jmol of these structures.

September 2010, David Goodsell

About Molecule of the Month
The RCSB PDB Molecule of the Month by David S. Goodsell (The Scripps Research Institute and the RCSB PDB) presents short accounts on selected molecules from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details.More