Heparanase

Heparanase is an endo-β-D-glucuronidase that catalyzes the hydrolytic cleavage of the β-1,4-glycosidic bond between a D-glucuronate and a D-glucosamine in heparan sulfate. The physiological role of heparanase is simply to degrade heparan sulfate but this activity can take many turns, as described in the review articles listed below.

The reaction mechanism probably involves general acid/base catalysis by Glu225 and nucleophilic catalysis by Glu343:
Glu225 protonates the oxygen of the glycosidic bond, and Glu343 performs a nucleophilic attack on the anomeric carbon to break the glycosidic bond and form an unstable ester intermediate. The ester is hydrolyzed by an incoming water molecule and Glu225 now acts as a general base to activate the water and regain a proton.

It is known that the antithrombin binding motif found in heparin is a substrate for heparanase, but since this structure is very rare in the natural substrate heparan sulfate, there is still much to find out about the substrate specificity of heparanase. Which O-sulfation patterns promote or inhibit catalysis? And which N-substituents?

Some of these questions were addressed using in vitro-generated heparan sulfate libraries and purified octasaccharides:
Gong, F., Jemth, P., Escobar Galvis, M. L., Vlodavsky, I., Horner, A., Lindahl, U., and Li, J.-P. (2003) Processing of macromolecular heparin by heparanase. J. Biol. Chem. 278, 35152-35158 [abstract]