Biochemistry—Shared Features of Protease Classes Which common mechanistic features are shared by serine proteases and aspartate (aspartyl) proteases?

Introduction / Context:
Protease families achieve peptide bond hydrolysis using different active-site chemistries, yet they share several mechanistic themes. Recognizing these shared features aids in understanding catalysis, substrate recognition, and inhibitor design across protease classes.

Given Data / Assumptions:

• Serine proteases use a Ser-His-Asp triad and form a transient acyl-enzyme intermediate; water is required for deacylation.
• Aspartate proteases (e.g., pepsin family, HIV protease) use two Asp residues to activate a water molecule for direct nucleophilic attack.
• Both enzyme classes recognize specific sequence contexts around the scissile bond (S1, S1′, etc.).

Concept / Approach:
Check each statement for validity across both families. Water involvement is universal for hydrolysis; base-assisted activation of the nucleophile occurs via His (serine proteases) or via Asp residues that polarize and deprotonate water (aspartate proteases). Sequence specificity arises from substrate-binding pockets that accommodate side chains selectively.

Step-by-Step Solution:

Verification / Alternative check:
Active-site structures and kinetic isotope effects support base-assisted proton transfers in both classes; substrate profiling defines sequence preferences.

Why Other Options Are Wrong:

• Each of A–C is correct; therefore D is correct and E is incorrect.

Common Pitfalls:
Assuming that only serine proteases use a base or that only one class shows sequence specificity; ignoring the different identities of the base (His vs Asp pair).

Final Answer:
All of the above