3.4.3 Glyceraldehyde-3-phosphate dehydrogenase

Glyceraldehyde-3-phosphate dehydrogenase provides a straightforward example of another type of enzyme catalysis, known as covalent catalysis. This reaction mechanism (Figure 3.4.3-1) is very common in dehydrogenation reactions, e.g. in the citric acid cycle and in the β-oxidation of fatty acids. The reaction goes through the following steps (cf. Figure 3.4.3-1b):

The substrate binds to the active site, where NAD⁺ is already bound.
A deprotonated cysteine thiol group (–S^–) in the active site performs a nucleophilic attack on the aldehyde carbon, which yields a tetrahedral intermediate state in which the enzyme and the substrate are covalently bound to each other (hence the name covalent catalysis).
The intermediate transfers 2 electrons and a proton to NAD⁺, yielding NADH and a thioester.
NADH leaves and is replaced by NAD⁺.
The thioester is cleaved by a phosphate ion, again by nucleophilic attack.
The product (1,3-bisphosphoglycerate) leaves, and the enzyme is restored to its original state.

The redox cosubstrate used by glyceraldehyde-3-phosphate dehydrogenase, nicotinamide adenine dinucleotide (NAD⁺), is the major acceptor of hydrogen abstracted from substrates throughout glycolysis and the citric acid cycle. Its structure and its reduction by hydrogen are shown in Figure 3.4.3-2. As you can see, all the action occurs at the nicotinamide moiety. The adenosine part is completely out of the picture, as far as the redox chemistry is concerned. Why, then, is it there at all? One answer is that it serves as a 'tag', an identifier that enables the coenzyme to interact with a defined set of enzymes. There is a second, very similar coenzyme, NADP⁺, which performs the same redox chemistry but has a different tag with an extra phosphate group (Figure 3.4.3-2a) and is used by a different set of enzymes. The reasons for this are discussed in a later chapter (see section 9.2).¹

1: However, it is interesting to note that, as in many other cosubstrates, the tag consists of a nucleotide instead of a peptide. This likely hearkens back to the RNA world—cosubstrates or coenzymes can't evolve as easily as enzymes, since they interact with many different enzymes and are therefore subject to a large number of constraints.