This reaction is typified by the formation of a Schiff base intermediate with a lysine residue (lysine 229) in the active site of the enzyme; the formation of a Schiff base is the key differentiator between Class I (produced by animals) and Class II (produced by fungi and bacteria) aldolases.

Each subunit has a molecular weight of 36 kDa and contains an eight-stranded α/β barrel, which encloses lysine 229 (the Schiff-base forming amino acid that is key for catalysis).

[13] Aldolase B plays a key role in carbohydrate metabolism as it catalyzes one of the major steps of the glycolytic-gluconeogenic pathway.

Though it does catalyze the breakdown of glucose, it plays a particularly important role in fructose metabolism, which occurs mostly in the liver, renal cortex, and small intestinal mucosa.

After glyceraldehyde is phosphorylated by triose kinase to form G3P, both products can be used in the glycolytic-gluconeogenic pathway, that is, they can be modified to become either glucose or pyruvate.

Due to the lack of functional aldolase B, organisms with HFI cannot properly process F1P, which leads to an accumulation of F1P in bodily tissues.

The loss of ATP leads to a multitude of problems including inhibition of protein synthesis and hepatic and renal dysfunction.

[14][18] Mutant alleles are a result of a number different types of mutations including base pair substitutions and small deletions.

The most common mutation is A149P, which is a guanine to cytosine transversion in exon 5, resulting in the replacement of alanine at position 149 with proline.