Molecule of the Month: Pepsin
Pepsin digests proteins in strong stomach acid
A Tricky Business
A Piece of Scientific History
The acid proteases have evolved to fill several functional roles in different organisms. Pepsin, shown at upper left (PDB entry 5pep ), is optimized for digestion of food in the acidic environment of the stomach. It is very promiscuous, cleaving proteins in many different places. Chymosin, shown at upper right (PDB entry 4cms ), is made by young calves to break down milk proteins. A purified form of chymosin, taken from calf stomach, has been used for centuries to curdle milk in the production of cheese. Cathepsin D, shown at lower left (PDB entry 1lyb ), digests proteins inside lysozomes, the tiny stomachs inside cells. Other cellular acid proteases, such as renin (not shown, PDB entry 1hrn ), are designed to make very specific cuts in one particular protein, aiding in the maturation of a hormone or structural protein. Endothiapepsin, shown at lower right (PDB entry 4ape ), is made by a fungus and excreted into the surrounding environment, breaking up the surrounding proteins and allowing the fungus to feed on the pieces.
Exploring the Structure
Pepsin and Pepstatin
Pepsin (PDB entry 1pso) uses a pair of aspartate residues to perform the protein cleavage reaction, shown here with red oxygen atoms. In an example of parallel evolution (where two organisms independently develop the same method for solving a problem), the mechanism is similar to that used by HIV protease. This structure also includes a non-cleavable inhibitor in the active site (shown in orange). It contains a hydroxyl group, shown here in purple, that mimics the place that water attaches during the cleavage reaction. Three crosslinks that strengthen the folded protein are also shown, formed between sulfur atoms (yellow) in cysteine. To explore this structure in more detail, click on the image for an interactive JSmol.
December 2000, David Goodsellhttp://doi.org/10.2210/rcsb_pdb/mom_2000_12