Wednesday, April 18, 2007

The Structure of the Pyruvate Dehydrogenase Complex

The pyruvate dehydrogenase complex catalyzes the reaction that converts pyruvate to acetyl-CoA with the release of CO2. The reaction is coupled to the reduction of NAD+ to NADH2 [Pyruvate Dehydrogenase Reaction]. The three components of the complex, E1, E2, and E3 catalyze different steps.

The size of the pyruvate dehydrogenase complex is enormous. It is several times bigger than a ribosome. In bacteria these complexes are located in the cytosol and in eukaryotic cells they are found in the mitochondrial matrix. Pyruvate dehydrogenase complexes are also present in chloroplasts.

The eukaryotic pyruvate dehydrogenase complex is the largest multienzyme complex known. The core of the complex is formed from 60 E2 subunits arranged in the shape of a pentagonal dodecahedron (12 pentagons joined at their edges to form a ball). This shape has 20 vertices and each vertex is occupied by an E2 trimer. Each of the E2 subunits has a linker region projecting upward from the surface. This linker contacts an outer ring of E1 subunits that surround the inner core. The linker region contains the lipoamide swinging arm.

The outer shell has 60 E1 subunits. Each E1 enzyme contacts one of the underlying E2 enzymes and makes additional contacts with its neighbors. The E1 enzyme consists of two α subunits and two β subunits (α2β2) so it is considerably larger than the E2 enzyme of the core. The E3 enzyme (an α2 dimer) lies in the center of the pentagon formed by the core E2 enzymes. There are 12 E3 enzymes in the complete complex corresponding to the 12 pentagons in the pentagonal dodecahedron shape. In eukaryotes, the E3 enzymes are associated with a small binding protein (BP) that’s part of the complex.

The model shown above has been constructed from high resolution electron microscopy images of pyruvate dehydrogenase complexes at low temperature (cryo-EM) (below). In this technique, a large number of individual images are combined and a three-dimensional image is built with the help of a computer. The model is then matched with the structures of any of the individual subunits that have been solved by X-ray crystallography or NMR.

A similar pyruvate dehydrogenase complex is present in many species of bacteria although some, such as gram negative bacteria, have a smaller version where there are only 24 E2 enzymes in the core. In these bacteria, the core enzymes are arranged as a cube with one trimer at each of the 8 vertices. The E2 subunits of the two different bacterial enzymes and the eukaryotic mitochondrial and chloroplast versions are all closely related. However, the gram negative bacterial enzymes contain E1 enzymes that are unrelated to the eukaryotic versions.

So far, it has not been possible to grow large crystals of the entire pyruvate dehydrogenase complex on Earth. Experiments were undertaken to grow crystals on the International Space Station where the absence of gravity might have led to better results. Unfortunately, none of the esperiments were successful so, for the time being, the best model of the pyruvate dehydrogenase complex is the one constructed from the cryo-EM images.

[This is a slightly modified version of material in Horton et al. (2006) Principles of Biochemistry 4th ed.©L.A. Moran and Pearson/Prentice Hall]


  1. Yesterday I saw a statement that PDH must have been formed abiogenetically. I cannot lay my hand on the source and while searching I stumbled onto your site.

    If PDH was created during abiogenesis, it implies that life cannot exist without it. That seems fair since the breakdown of pyruvate to acetyl CoA is vital. Yet the complexity of PDH, and all the comings and goings around it is certainly an indication that it is too good to have been generated spontaneously.

    And if abiogenesis created a cell that had PDH, it would need that information in a genetic code to be able to reproduce that enzyme. This requires orders of greater complexity.

    Evolution is not science, it is a religion that requires more faith than any other.

    Martin Bredenkamp

  2. @Martin Bredenkamp,

    Th original reaction was catalyzed by an enzyme called pyruvate:ferredoxin 2-oxidoreductase (EC This enzyme is much simpler and it uses a small iron-sulfur protein (ferredoxin) as a cosubstrate. Many early branching bacteria still use this enzyme instead of the more complex enzyme, pyruvate dehydrogenase (PDH), suggesting that it is the primitive enzyme.

    There are many examples of simple enzymes that use iron as the oxidation/reduction agent and many examples of these enzymes being replaced in later-evolving species.

    PDH probably arose from a series of enzymes required for synthesizing branched chain amino acids. This is explained in most biochemistry textbooks but I understand why you don't know this. It's because creationists never read science textbooks—they prefer to just make things up.

    Incidentally, it's the reverse reaction—catalyzed efficiently by pyruvate:ferredoxin oxidoreductase—that would have been important in ancient species. The reverse reaction is a way of fixing carbon dioxide and creating three-carbon compounds.

  3. Why has no EM data for the E1-E2-E3 complex been reported?

    And how can the E2-E1 and E2-E3 be made?

    Also how was the E2 core domain prepared recombinantly? and starting from crude extracts?