3ILR
Structure of Heparinase I from Bacteroides thetaiotaomicron in complex with tetrasaccharide product
Summary for 3ILR
| Entry DOI | 10.2210/pdb3ilr/pdb |
| Related | 3IKW |
| Descriptor | Heparin lyase I, 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(4-1)-4-deoxy-2-O-sulfo-beta-D-erythro-hex-4-enopyranuronic acid, 4-deoxy-2-O-sulfo-beta-D-erythro-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose, ... (6 entities in total) |
| Functional Keywords | heparin, polysaccharide lyase, beta-jelly roll, lyase |
| Biological source | Bacteroides thetaiotaomicron |
| Total number of polymer chains | 1 |
| Total formula weight | 43432.58 |
| Authors | Garron, M.L.,Cygler, M.,Shaya, D. (deposition date: 2009-08-07, release date: 2009-09-29, Last modification date: 2024-02-21) |
| Primary citation | Han, Y.H.,Garron, M.L.,Kim, H.Y.,Kim, W.S.,Zhang, Z.,Ryu, K.S.,Shaya, D.,Xiao, Z.,Cheong, C.,Kim, Y.S.,Linhardt, R.J.,Jeon, Y.H.,Cygler, M. Structural snapshots of heparin depolymerization by heparin lyase I. J.Biol.Chem., 284:34019-34027, 2009 Cited by PubMed Abstract: Heparin lyase I (heparinase I) specifically depolymerizes heparin, cleaving the glycosidic linkage next to iduronic acid. Here, we show the crystal structures of heparinase I from Bacteroides thetaiotaomicron at various stages of the reaction with heparin oligosaccharides before and just after cleavage and product disaccharide. The heparinase I structure is comprised of a beta-jellyroll domain harboring a long and deep substrate binding groove and an unusual thumb-resembling extension. This thumb, decorated with many basic residues, is of particular importance in activity especially on short heparin oligosaccharides. Unexpected structural similarity of the active site to that of heparinase II with an (alpha/alpha)(6) fold is observed. Mutational studies and kinetic analysis of this enzyme provide insights into the catalytic mechanism, the substrate recognition, and processivity. PubMed: 19801541DOI: 10.1074/jbc.M109.025338 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.5 Å) |
Structure validation
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