Crystal structure of chondroitinase B from Flavobacterium heparinum and its complex with a disaccharide product at 1.7 angstrom resolution

Glycosaminoglycans (GAGs) are a family of acidic heteropolysaccharides, inc luding such molecules as chondroitin sulfate, dermatan sulfate, heparin and keratan sulfate. Cleavage of the O-glycosidic bond within GAGs can be acco mplished by hydrolases as well as lyases, yielding disaccharide and oligosa ccharide products. We have determined the crystal structure of chondroitina se B, a glycosaminoglycan lyase from Flavobacterium heparinum, as well as i ts complex with a dermatan sulfate disaccharide product, both at 1.7 Angstr om resolution. Chondroitinase B adopts the right-handed parallel beta-helix fold, found originally in pectate lyase and subsequently in several polysa ccharide lyases and hydrolases. Sequence homology between chondroitinase B and a mannuronate lyase from Pseudomonas sp. suggests this protein also ado pts the beta-helix fold. Binding of the disaccharide product occurs within a positively charged cleft formed by loops extending from the surface of th e beta-helix. Amino acid residues responsible for recognition of the disacc haride, as well as potential catalytic residues, have been identified. Two arginine residues, Arg318 and Arg364, are found to interact with the sulfat e group attached to O-4 of N-acetylgalactosamine. Cleavage of dermatan sulf ate likely occurs at the reducing end of the disaccharide, with Glu333 poss ibly acting as the general base. (C) 1999 Academic Press.