3IN9

Crystal structure of heparin lyase I complexed with disaccharide heparin

3IN9 の概要

• エントリーDOI: 10.2210/pdb3in9/pdb
• 関連するPDBエントリー: 3IMN 3INA
• 関連するBIRD辞書のPRD_ID: PRD_900026
• 分子名称: Heparin lyase I, 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose, CALCIUM ION, ... (4 entities in total)
• 機能のキーワード: jelly roll, lyase
• 由来する生物種: Bacteroides thetaiotaomicron
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 44029.38

構造登録者

Han, Y.H.,Ryu, K.S.,Kim, H.Y.,Jeon, Y.H. (登録日: 2009-08-12, 公開日: 2009-09-29, 最終更新日: 2023-11-01)

主引用文献

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

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: 19801541
DOI: 10.1074/jbc.M109.025338

実験手法

X-RAY DIFFRACTION (2 Å)