1DBO

CRYSTAL STRUCTURE OF CHONDROITINASE B

Summary for 1DBO

• Entry DOI: 10.2210/pdb1dbo/pdb
• Related: 1DBG
• Descriptor: CHONDROITINASE B, 4-deoxy-alpha-D-glucopyranose-(1-3)-[beta-D-glucopyranose-(1-4)]2-O-methyl-beta-L-fucopyranose-(1-4)-beta-D-xylopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose, 4-deoxy-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose, ... (4 entities in total)
• Functional Keywords: active site, beta-elimination, dematan sulfate, lyase
• Biological source: Pedobacter heparinus
• Total number of polymer chains: 1
• Total formula weight: 57956.69

Authors

Huang, W.,Matte, A.,Li, Y.,Kim, Y.S.,Linhardt, R.J.,Su, H.,Cygler, M. (deposition date: 1999-11-03, release date: 2000-01-12, Last modification date: 2024-10-30)

Primary citation

Huang, W.,Matte, A.,Li, Y.,Kim, Y.S.,Linhardt, R.J.,Su, H.,Cygler, M.
Crystal structure of chondroitinase B from Flavobacterium heparinum and its complex with a disaccharide product at 1.7 A resolution.
J.Mol.Biol., 294:1257-1269, 1999

PubMed Abstract: Glycosaminoglycans (GAGs) are a family of acidic heteropolysaccharides, including such molecules as chondroitin sulfate, dermatan sulfate, heparin and keratan sulfate. Cleavage of the O-glycosidic bond within GAGs can be accomplished by hydrolases as well as lyases, yielding disaccharide and oligosaccharide products. We have determined the crystal structure of chondroitinase B, a glycosaminoglycan lyase from Flavobacterium heparinum, as well as its complex with a dermatan sulfate disaccharide product, both at 1.7 A resolution. Chondroitinase B adopts the right-handed parallel beta-helix fold, found originally in pectate lyase and subsequently in several polysaccharide lyases and hydrolases. Sequence homology between chondroitinase B and a mannuronate lyase from Pseudomonas sp. suggests this protein also adopts the beta-helix fold. Binding of the disaccharide product occurs within a positively charged cleft formed by loops extending from the surface of the beta-helix. Amino acid residues responsible for recognition of the disaccharide, as well as potential catalytic residues, have been identified. Two arginine residues, Arg318 and Arg364, are found to interact with the sulfate group attached to O-4 of N-acetylgalactosamine. Cleavage of dermatan sulfate likely occurs at the reducing end of the disaccharide, with Glu333 possibly acting as the general base.

PubMed: 10600383
DOI: 10.1006/jmbi.1999.3292

Experimental method

X-RAY DIFFRACTION (1.7 Å)