Heparinase II C-terminal domain. Heparinase II (HepII) is an 85-kDa dimeric enzyme that depolymerizes both heparin and heparan sulfate glycosaminoglycans. The protein is composed of three domains: an N-terminal alpha-helical domain, a central two-layered beta-sheet domain, and a C-terminal domain forming a two-layered beta-sheet. The C-terminal domain contains nine beta-strands packed together in a manner resembling a beta-barrel.

Carbohydrate Binding Module 6 (CBM6) and CBM35_like superfamily. Carbohydrate binding module family 6 (CBM6, family 6 CBM), also known as cellulose binding domain family VI (CBD VI), and related CBMs (CBM35 and CBM36). These are non-catalytic carbohydrate binding domains found in a range of enzymes that display activities against a diverse range of carbohydrate targets, including mannan, xylan, beta-glucans, cellulose, agarose, and arabinans. These domains facilitate the strong binding of the appended catalytic modules to their dedicated, insoluble substrates. Many of these CBMs are associated with glycoside hydrolase (GH) domains. CBM6 is an unusual CBM as it represents a chimera of two distinct binding sites with different modes of binding: binding site I within the loop regions and binding site II on the concave face of the beta-sandwich fold. CBM36s are calcium-dependent xylan binding domains. CBM35s display conserved specificity through extensive sequence similarity, but divergent function through their appended catalytic modules. This alignment model also contains the C-terminal domains of bacterial insecticidal toxins, where they may be involved in determining insect specificity through carbohydrate binding functionality.

Heparinase II/III-like protein. This family features sequences that are similar to a region of the Flavobacterium heparinum proteins heparinase II and heparinase III. The former is known to degrade heparin and heparin sulphate, whereas the latter predominantly degrades heparin sulphate. Both are secreted into the periplasmic space upon induction with heparin.

ChainA, heparinase II protein [Pedobacter heparinus],2FUQ_B Chain B, heparinase II protein [Pedobacter heparinus]

Structureof Heparinase II complexed with heparan sulfate degradation disaccharide product [Pedobacter heparinus],3E80_B Structure of Heparinase II complexed with heparan sulfate degradation disaccharide product [Pedobacter heparinus],3E80_C Structure of Heparinase II complexed with heparan sulfate degradation disaccharide product [Pedobacter heparinus]

ChainA, Heparinase II protein [Pedobacter heparinus],3E7J_B Chain B, Heparinase II protein [Pedobacter heparinus]

ChainA, heparinase II protein [Pedobacter heparinus],2FUT_B Chain B, heparinase II protein [Pedobacter heparinus]

Heparin and heparin-sulfate lyase OS=Pedobacter heparinus (strain ATCC 13125 / DSM 2366 / CIP 104194 / JCM 7457 / NBRC 12017 / NCIMB 9290 / NRRL B-14731 / HIM 762-3) OX=485917 GN=hepB PE=1 SV=1