3ikw | pdb_00003ikw

Structure of Heparinase I from Bacteroides thetaiotaomicron

spinqualitylabelsall models 3ikw, resolution 1.30Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3ikw is a 1 chain structure with sequence from Bacteroides thetaiotaomicron. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CA, EDO Gene: BT_4675 (Bacteroides thetaiotaomicron) Activity: Heparin lyase, with EC number 4.2.2.7 Resources: FirstGlance, OCA, RCSB, PDBsum Publication Abstract from PubMed 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. Structural snapshots of heparin depolymerization by heparin lyase I.,Han YH, Garron ML, Kim HY, Kim WS, Zhang Z, Ryu KS, Shaya D, Xiao Z, Cheong C, Kim YS, Linhardt RJ, Jeon YH, Cygler M J Biol Chem. 2009 Dec 4;284(49):34019-27. Epub 2009 Oct 2. PMID:19801541 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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