Question

Cysteine proteases are catalytically homologous to serine proteases, where the active site serine is replaced with a cysteine. What would be the appropriate order of the mechanism? Just write the numbers in order.

1. Peptide bond is cleaved and C becomes sp2
2. The acyl-enzyme is formed by the transfer of the proton from the positively charged histidine residue, acting as a general acid, to the amino group of the substrate.
3. The side-chain of the amino acid residue immediately before the scissile peptide bond binds to the specificity pocket on the enzyme.
4. Histidine acts as a general base to draw a proton away from cysteine.
5. Amino component of the peptide substrate is released as product.
6. The sulfur of the cysteine nucleophillically attacks the sp2 carbonyl carbon of the scissile peptide bond.
7. Histidine acts as a general base to draw a proton away from water.
8. Carboxylic acid component of the peptide substrate is released as product.
9. The cysteine-peptide bond breaks creating a sp2 carboxylic acid product.
10. OH- nucleophillically attacks the sp2 carbonyl carbon of the scissile peptide bond
11. Sp3 carbon intermediate is formed and the unstable negatively charged oxygen is stabilized via interactions with the NH groups in the oxyanion hole.

Answer 1

1. Histidine acts as a general base to draw a proton away from water.
2. OH- nucleophillically attacks the sp2 carbonyl carbon of the scissile peptide bond
3. The side-chain of the amino acid residue immediately before the scissile peptide bond binds to the specificity pocket on the enzyme.
4. Sp3 carbon intermediate is formed and the unstable negatively charged oxygen is stabilized via interactions with the NH groups in the oxyanion hole.
5. The acyl-enzyme is formed by the transfer of the proton from the positively charged histidine residue, acting as a general acid, to the amino group of the substrate.
6. The sulfur of the cysteine nucleophillically attacks the sp2 carbonyl carbon of the scissile peptide bond.
7. Peptide bond is cleaved and C becomes sp2
8. The cysteine-peptide bond breaks creating a sp2 carboxylic acid product.
9. Amino component of the peptide substrate is released as product.
10. Histidine acts as a general base to draw a proton away from cysteine.
11. Carboxylic acid component of the peptide substrate is released as product.