Class I aldolase (Schiff base) template

Fructose 1,6-bisphosphate (open chain) forms a protonated Schiff base with Lys229; Asp33 removes the C4–OH proton, the C3–C4 bond breaks with the iminium as electron sink to release glyceraldehyde 3-phosphate, and the enamine is protonated and hydrolysed to dihydroxyacetone phosphate.

Mechanism step by step

Lys229 forms an iminium ion with fructose 1,6-bisphosphate; a retro-aldol cleavage of C3–C4 releases GAP

1. Lys229 adds to C2 – The ε-amino group attacks the ketone: a carbinolamine (zwitterion)
2. Iminium ion – Proton transfers and loss of water: the protonated Schiff base (arrows not shown)
3. Retro-aldol cleavage – Asp33 takes the C4–OH proton; C3–C4 breaks and the iminium takes the electrons
4. Enamine protonation – C3 takes a proton: the iminium ion of DHAP
5. Hydrolysis (summarised) – Water adds to C=N⁺ and Lys229 leaves: DHAP and free enzyme

Key points

• The protonated Schiff base (iminium) is a better electron sink than C=O, so it stabilises the C3 carbanion/enamine (Horecker: NaBH₄ traps it on Lys).
• Class II aldolases (bacteria, fungi) use Zn²⁺ instead of a Schiff base to polarise the carbonyl.
• ΔG°′ = +23.8 kJ/mol, yet in cells ΔG ≈ 0 because the products are removed and kept at low concentration.
• In gluconeogenesis the same enzyme runs the aldol forward: DHAP + GAP → fructose 1,6-bisphosphate.

Drawn with 235 atoms, 15 arrows, 8 shapes – every one editable in MolDraw.

Sources

• Nelson & Cox, Lehninger Principles of Biochemistry, 8th ed., 2021, ch. 14 Textbook
• Berg, Tymoczko, Gatto & Stryer, Biochemistry, 9th ed., 2019, ch. 16 Textbook
• Grazi, Rowley, Cheng, Tchola & Horecker, Biochem. Biophys. Res. Commun. 1962, 9, 38 Original paper