5.1 Pyruvate dehydrogenase

Subsections:
5.1.1 Catalytic mechanisms in the pyruvate dehydrogenase reaction
5.1.2 Regulation of pyruvate dehydrogenase

Pyruvate dehdrogenase catalyzes a the following reaction:

pyruvate + coenzyme A + NAD⁺→ acetyl-CoA + NADH + H⁺ + CO₂

This reaction does not occur all at once but instead comprises sequence of group transfers and redox steps. We can distinguish five steps altogether, which involve an equal number of coenzymes. The five reaction steps occur at three different active sites, which are located on three different types of enzyme subunits, which are bundled together into one large functional complex. Pyruvate dehydrogenase therefore is a multi-enzyme complex.

There are multiple copies of each of the three individual enzymes. The number of subunits totals sixty in the E.coli version of pyruvate dehydrogenase (Figure 5.1-1) and is even higher in mammalian enzymes. Nevertheless, within this large assembly, each subunit of any type is within easy reach of ones of the other two types. This proximity ensures an easy flow of intermediate substrates from one active site to the next during the sequential stages of the reaction, which greatly increases the overall throughput. This increased throughput is a key advantage of multi-enzyme complexes.

The individual subunits are named according to the specific partial reactions they catalyze. The first subunit is called pyruvate dehydrogenase, which term therefore is ambiguous, denoting both the entire complex and the first of the subunits. The second subunit is called dihydrolipoyl transacetylase, and the third one dihydrolipoyl dehydrogenase. Instead of these explicit names, we will use a common shorthand notation and call them E₁, E₂ and E₃ in the following.

Figure 5.1-2 gives an overview of the sequential steps of the pyruvate dehydrogenase reaction:

Pyruvate is decarboxylated, and the remaining hydroxyethyl group becomes covalently bound to the TPP coenzyme at E₁.
The hydroxyethyl group is transferred to lipoamide, and is concomitantly dehydrogenated to an acetyl group. This still occurs in the active site of E₁.
The acetyl group is transferred from lipoamide to coenzyme A; this occurs in the active site of E₂.
Lipoamide is reoxidized, and the hydrogen is transferred to flavine adenine dinucleotide (FAD) within the active site of E₃.
FADH₂ is reoxidized, and the hydrogen is transferred to NAD⁺. This step is catalyzed by E₃, too. NADH is then released from the enzyme.

As you can see, each step in the pyruvate dehydrogenase reaction involves one or more coenzymes. Therefore, this enzyme illustrates quite nicely the great importance of coenzymes in enzyme catalysis.