PepsinDecember 2000 Molecule of the Month by David Goodsell
doi: 10.2210/rcsb_pdb/mom_2000_12 (PDF Version, ePub Version )
During the holiday season, we often place greater demands on our digestive enzymes than at other times of the year. Our digestive system contains a host of tough, stable enzymes designed to seek out those rich holiday treats and break them into small pieces. Pepsin is the first in a series of enzymes that digest proteins. In the stomach, protein chains bind in the deep active site groove of pepsin, seen in the upper illustration (from PDB entry 5pep), and are broken into smaller pieces. Then, a variety of proteases and peptidases in the intestine finish the job. The small fragments--amino acids and dipeptides--are then absorbed by cells for use as metabolic fuel or construction of new proteins.
A Tricky Business
Enzymes that digest proteins pose a real challenge. The enzyme must be constructed inside the cell, but controlled in some manner so that it doesn't immediately start digesting the cell's own proteins. To solve this problem, pepsin and many other protein-cutting enzymes are created as inactive "proenzymes," which may then be activated once safely outside the cell. Pepsin is constructed with an extra 44 amino acids, shown in green in the lower illustration (from entry 3psg), which block the large active site groove and hobble the enzyme. In the stomach, this extraneous chain is clipped off and the enzyme begins its destructive campaign.
A Piece of Scientific History
For several reasons, digestive enzymes are attractive candidates for scientific study. They are easily isolated and present in large amounts in digestive juices. They are also extraordinarily stable, because they perform their jobs under the harsh conditions present in the digestive system. The reactions catalyzed by digestive enzymes are also easily followed: you can add them to a protein such as gelatin and watch it lose its gel-like consistency. In the 18th century, pepsin was the first enzyme to be discovered, and later, pepsin was the second enzyme to be crystallized (after urease). These crystals played an important role in showing that enzymes were proteins and that they had a defined structure. Today, the structure of pepsin, determined from similar crystals, is available in PDB entry 5pep and several others.
Pepsin is one example of a group of enzymes termed "acid proteases." In the case of pepsin, this name is doubly
appropriate. Pepsin works its best in strong hydrochloric acid. But the similarity with the other enzymes pictured here refers
to a second type of acid. The active site of the acid proteases rely on two acidic aspartate amino acids, which activate a water
molecule and use it to cleave protein chains. These aspartates are pictured on the next page.
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 uses a pair of aspartate residues to perform the protein cleavage reaction. 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, discussed in a previous
Molecule of the Month. In the upper illustration, from PDB entry 5pep,
the active site aspartates are seen as spacefilling spheres at the center of the deep active site groove, in white and red. In the lower
illustration, three disulfide bridges are also shown. These crosslinks, formed between sulfur atoms (yellow) in cysteine amino acids,
strengthen the protein chain.
These illustrations were created with RasMol. You can create similar illustrations by clicking on the PDB accession code and going to "View Structure." To highlight the active site aspartates, select residues numbered 32 and 215 in this structure file.
© 2013 David Goodsell & RCSB Protein Data Bank