Molecule of the Month: Pyruvate Dehydrogenase Complex
A huge molecular complex links three sequential reactions for energy production
Anatomy of a Multienzyme Complex
Uncovering the Complex
Take Your Vitamins!
Exploring the Structure
Pyruvate Dehydrogenase (PDB entries 1eaa and 1b5s)
As is often the case in biology, things get even more complicated when you look closer. There are many variations on this basic structure in different types of cells. Some cells have one or two carrier domains on the little tails instead of the three shown here. The complex in our cells also includes another protein in the core, with its own carrier domains. Also, the core itself can have different geometry: a cube-shaped core composed of 24 subunits or a dodecahedral core composed of 60 subunits (shown here from PDB entry 1b5s ). To explore both of these types of cores, click on the image for an interactive Jmol.
Topics for Further Discussion
- More and more proteins are being discovered that include several functional domains connected by flexible linkers. Can you find other examples in the PDB?
- In the PDB, you can find many different enzymes that use cofactors derived from vitamins such as thiamine, niacin, and riboflavin. Do they all perform similar functions, or are the cofactors used in different ways?
Related PDB-101 Resources
- Browse Biological Energy
- Browse Enzymes
- D. L. Nelson and M. M. Cox (2008) Lehninger Principles of Biochemistry. Worth Publishers, New York.
- X. Yu, Y. Hiromasa, H. Tsen, J. K. Stoops, T. E. Roche and Z. H. Zhou (2008) Structures of the human pyruvate dehydrogeanse complex cores: a highly conserved catalytic center with flexible N-terminal domains. Structure 16, 104-114.
- J. L. S. Milne, X. Wu, M. J. Borgnia, J. S. Lengyel, B. R. Brooks, D. Shi, R. N. Perham and S. Subramaniam (2006) Molecular structure of a 9-MDa icosahedral pyruvate dehydroegnase subcomplex containing the E2 and E3 enzymes using cryoelectron microscopy. Journal of Biological Chemistry 281. 4364-4370
- T. Izard, A. Aevarsson, M. D. Allen, A. H. Westphal, R. N. Perham, A. deKok and W. G. J. Hol (1999) Principles of quasi-equivalence and Euclidean geometry govern the assembly of cubic and dodecahedral cores of pyruvate dehydrogenase complexes. Proceedings of the National Academy of Sciences USA 96, 1240-1245.
September 2012, David Goodsellhttp://doi.org/10.2210/rcsb_pdb/mom_2012_9