Proteolytic enzymes: General features of their mode of action

The three-dimensional structure of PNGase F, a glycosylasparaginase from Flavobacterium meningosepticum

BACKGROUND

Peptide:N-glycosidase F (PNGase F) is an enzyme that catalyzes the complete removal of N-linked oligosaccharide chains from glycoproteins. Often called an endoglycosidase, it is more correctly termed an amidase or glycosylasparaginase as cleavage is at the asparagine-sugar amide linkage. The enzyme is widely used in structure-function studies of glycoproteins.

RESULTS

We have determined the crystal structure of PNGase F at 1.8 A resolution. The protein is folded into two domains, each with an eight-stranded antiparallel beta jelly roll configuration similar to many viral capsid proteins and also found, in expanded form, in lectins and several glucanases. Two potential active site regions have been identified, both in the interdomain region and shaped by prominent loops from one domain. Exposed aromatic residues are a feature of one site.

CONCLUSIONS

The finding that PNGase F is based on two jelly roll domains suggests parallels with lectins and other carbohydrate-binding proteins. These proteins either bind sugars on the concave face of the beta-sandwich structure (aided by loops) or amongst the loops themselves. Further analysis of the function and identification of the catalytic site should lead to an understanding of both the specificity of PNGase F and possibly also the recognition processes that identify glycosylation sites on proteins.

Active site and catalytic mechanism of phospholipase A2

The esterolytic enzyme phospholipase A2 specificially splits the 2-acyl linkage of phosphoglycerides in a calcium-dependent reaction. In the pancreas the enzyme occurs as a zymogen which is activated on secretion into the duodenal tract by the removal of seven amino acid residues from the N terminus by trypsin. Having refined our X-ray analysis of the crystal structure of bovine pancreatic phospholipase A2 from 2.4 A (ref. 4) to 1.7 A resolution, we now describe how the structure of the molecule may account for the specificity of the enzyme and for the sudden and dramatic change in activity when the substrate concentration passes the critical micelle concentration.