Molecule of the Month: Isocitrate Dehydrogenase
Atomic structures have revealed the catalytic steps of a citric acid cycle enzyme
Different Approaches to the Same Task
Control by Phosphorylation
Exploring the Structure
Isocitrate Dehydrogenase (PDB entries 8icd, 9icd, 1ika, 3icd, 4icd, 1ide and 1idc )
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.
Topics for Further Discussion
- Structures are available for most of the enzymes in the citric acid cycle. Can you find them in the PDB?
- Isocitrate dehydrogenase can distinguish between the two stereoisomers of isocitrate. It does this by surrounding isocitrate and forming specific interactions with each of its functional groups. Can you find the amino acids in the protein that are important for these interactions? What role does the metal ion play? Be sure to use the biological unit when you look at this interaction, since the active site is formed between the two subunits.
Related PDB-101 Resources
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- J. Zheng and Z. Jia (2010) Structure of the bifunctional isocitrate dehydrogenase kinase/phosphatase. Nature 465, 961-965.
- A. B. Taylor, G. Hu, P. J. Hart and L. McAlister-Henn (2008) Allosteric motions in structures of yeast NAD+-specific isocitrate dehydrogenase. Journal of Biological Chemistry 283, 10872-10880.
- J. M. Bolduc, D. H. Dyer, W. G. Scott, P. Singer, R. M. Sweet, D. E. Koshland Jr. and B. L. Stoddard (1995) Mutagenesis and Laue structure of enzyme intermediates: isocitrate dehydrogenase. Science 268, 1312-1318.
- J. H. Hurley, A. M. Dean, D. E. Koshland Jr. and R. M. Stroud (1991) Catalytic mechanism of NADP+-dependent isocitrate dehydrogenase: implications from the structures of magnesium-isocitrate and NADP+ complexes. Biochemistry 30, 8671-8678.
September 2010, David Goodsellhttp://doi.org/10.2210/rcsb_pdb/mom_2010_9