Molecule of the Month: Pyruvate Kinase M2
Pyruvate kinases are the paradoxical gatekeepers for cancer cell metabolism and growth.
Pyruvate Kinase M2: The Gatekeeper
Energy Production Paradox
The Warburg Effect and Cancer Treatment
Exploring the Structure
Allosteric Regulation of Pyruvate Kinase
Structures of the PKM2 tetramer reveal how different small molecules cause allosteric shape changes in the protein that help regulate its action. The active form is shown at left (PDB ID 4fxf) with ATP, oxalate and magnesium in the active site, and fructose bisphosphate (FBP) in a regulatory site. The inactive form is at center with alanine in a regulatory site (PDB ID 6gg3)—notice that it has shifted shape and is now narrower through the middle. Researchers are actively looking for drug molecules that bind to PKM2, for use in cancer treatment. For example, an artificial activator molecule (magenta) is bound in the structure at right (PDB ID 3me3) along with FBP, shifting the molecule to the active form and hopefully reversing the Warburg Effect in cells treated with it.
Topics for Further Discussion
- Cell proliferation can also be slowed by inhibiting lactate dehydrogenase, and used to monitor cancer progression and treatment efficacy. Explore lactate dehydrogenase with a trial anticancer agent in PDB ID 4ajp.
- The PDB archive includes many structures of human PKM2 with different small molecules. To find them, try going to PDB entry 4fxf and in the “Macromolecules” panel, look for the section on UniProt and click “Find proteins for P14618.”
Related PDB-101 Resources
- Browse Cancer
- Browse Biological Energy
References
- Vaupel, P., Multhoff, G. (2021) Revisiting the Warburg effect: Historical dogma versus current understanding. The Journal of Physiology, 599, 1745–1757.
- 6wp3: Nandi, S., Razzaghi, M., Srivastava, D., Dey, M. (2020) Structural basis for allosteric regulation of pyruvate kinase M2 by phosphorylation and acetylation. Journal of Biological Chemistry, 295, 17425–17440.
- Alquraishi, M., Puckett, D. L., Alani, D. S., Humidat, A. S., Frankel, V. D., Donohoe, D. R., Whelan, J., Bettaieb, A. (2019) Pyruvate kinase M2: A simple molecule with complex functions. Free Radical Biology and Medicine, 143, 176–192.
- Macpherson, J. A., Theisen, A., Masino, L., Fets, L., Driscoll, P. C., Encheva, V., Snijders, A. P., Martin, S. R., Kleinjung, J., Barran, P. E., Fraternali, F., Anastasiou, D. (2019) Functional cross-talk between allosteric effects of activating and inhibiting ligands underlies PKM2 regulation. ELife, 8, e45068.
- 6gg3: Yuan, M., McNae, I. W., Chen, Y., Blackburn, E. A., Wear, M. A., Michels, P. A. M., Fothergill-Gilmore, L. A., Hupp, T., Walkinshaw, M. D. (2018) An allostatic mechanism for M2 pyruvate kinase as an amino-acid sensor. Biochemical Journal 475, 1821-1837.
- Israelsen, W. J., Vander Heiden, M. G. (2015) Pyruvate kinase: Function, regulation and role in cancer. Seminars in Cell & Developmental Biology, 43, 43–51.
- 3me3: Anastasiou, D., Yu, Y., Israelsen, W. J., Jiang, J. K., Boxer, M. B., Hong, B. S., Tempel, W., Dimov, S., Shen, M., Jha, A., Yang, H., Mattaini, K. R., Metallo, C. M., Fiske, B. P., Courtney, K. D., Malstrom, S., Khan, T. M., Kung, C., Skoumbourdis, A. P., Veith, H., Southall, N., Walsh, M. J., Brimacombe, K. R., Leister, W., Lunt, S. Y., Johnson, Z. R., Yen, K. E., Kunii, K., Davidson, S. M., Christofk, H. R., Austin, C. P., Inglese, J., Harris, M. H., Asara, J. M., Stephanopoulos, G., Salituro, F. G., Jin, S., Dang, L., Auld, D. S., Park, H. W., Cantley, L. C., Thomas, C. J., Vander Heiden, M. G. (2012) Pyruvate kinase M2 activators promote tetramer formation and suppress tumorigenesis. Nature Chemical Biology 8, 839-847.
- Vander Heiden, M., Cantley, L., Thompson, C. (2009) Understanding the Warburg effect: The metabolic requirements of cell proliferation. Science, 324, 1029–1033.
- 4fxf: Pan, Y. H., Epstein, T. M., Jain, M. K., Bahnson, B.J. (2001) Five coplanar anion binding sites on one face of phospholipase A2: relationship to interface binding. Biochemistry 40, 609-617.
June 2022, Faiza Ahmed, Jonathan Ash, Thirth Patel, Auriel Sanders, David Goodsell, Shuchismita Dutta
http://doi.org/10.2210/rcsb_pdb/mom_2022_6