Molecule of the Month: Legumain

Legumain has been given many names, reflecting its many different functions. In plants, it helps to process proteins in storage vacuoles, so it has been called vacuolar processing enzyme. In our cells, it processes proteins for the immune system, generating the short peptides displayed by MHC, and has been called asparaginyl endopeptidase (based on its preference for cleaving proteins after asparagine). It also acts as an enzyme that chews off amino acids at the end of protein chains, and was given another name for that function. Fortunately, the research world has settled down to the simpler name “legumain” to refer to the enzyme that performs all of these jobs.

Legumain (shown here from PDB entry 4awb) uses a cysteine amino acid to perform its protein-cutting reaction, assisted by a histidine and an asparagine. However, these three amino acids are arranged differently than the familiar catalytic triad seen in serine proteases. In serine proteases, all three are arranged in a line on one side of the target protein chain, and in legumain, the cysteine and the histidine/asparagine attack the chain from opposite sides. Caspases have a similar arrangement of catalytic amino acids, but the cysteine protease papain has an arrangement more like the serine proteases. Legumain also has a small specificity pocket with two negatively-charged amino acids and two positively-charged amino acids. These amino acids recognize an asparagine sidechain in the target protein, ensuring that legumain only cuts in the proper place.

Surprisingly, further study of legumain revealed that it is also quite adept at reconnecting protein chains. For example, it is involved in the circular permutation of concanavalin A, and also assists with building of cyclic peptides that are used by plants for defense. This ligation reaction occurs in the same active site, but doesn’t appear to use the cysteine amino acid. Instead, a nearby aspartate adopts an unusual chemical form (shown in the JSmol) and is thought to assist with the reaction.

Proteases can be dangerous to the cell if not properly controlled. Legumain is produced by ribosomes as an inactive proenzyme (PDB entry 4fgu), with a long inhibitory portion that blocks the active site. Legumain typically performs its function in vacuoles or endosomes, where other protein-cutting enzymes clip off the extra portion to activate it. One type of plant legumain (PDB entry 5nij) adds an extra step to this maturation process: the cleaved version stays together, and then further assembles into dimers and larger aggregates, which are stored in the endoplasmic reticulum until they are needed.