Serine protease (chymotrypsin) template

Chymotrypsin cuts a peptide bond in two half-reactions: Ser195 (activated by His57, held by Asp102) attacks the carbonyl to give a tetrahedral intermediate in the oxyanion hole, the amine leaves to give the acyl-enzyme, and water hydrolyses the ester the same way.

Mechanism step by step

The catalytic triad Asp102–His57–Ser195: a tetrahedral intermediate, an acyl-enzyme, then hydrolysis by water

1. Acylation: attack – His57 takes the Ser195 proton as Ser–O attacks the C=O; Asp102 holds His57–H⁺ in place
2. Acyl-enzyme – The O⁻ (in the oxyanion hole) re-forms C=O; the amine N takes H⁺ from His57 and leaves
3. Deacylation: water attacks – His57 now activates water; a second tetrahedral intermediate
4. Release – C=O re-forms, Ser195 leaves and takes back its proton: free enzyme

Key points

• Ser195 is made a strong nucleophile by His57 (general base); Asp102 orients His57 and stabilises His57–H⁺ (charge-relay system, Blow et al. 1969).
• The oxyanion of the tetrahedral intermediate is H-bonded by the backbone NHs of Gly193 and Ser195 (the oxyanion hole), which binds the transition state more tightly than the substrate.
• Ping-pong kinetics: the amine leaves before water enters; the covalent acyl-enzyme can be trapped (burst kinetics with p-nitrophenyl acetate).
• The S1 pocket sets specificity: large hydrophobic side chains (Phe, Tyr, Trp) for chymotrypsin, Lys/Arg for trypsin (Asp189), small ones for elastase.

Drawn with 124 atoms, 17 arrows, 8 shapes – every one editable in MolDraw.

Sources

• Nelson & Cox, Lehninger Principles of Biochemistry, 8th ed., 2021, ch. 6 Textbook
• Berg, Tymoczko, Gatto & Stryer, Biochemistry, 9th ed., 2019, ch. 9 Textbook
• Blow, Birktoft & Hartley, Nature 1969, 221, 337 Original paper