Structural snapshots of heparin depolymerization by heparin lyase I.
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.
Han
Young-Hyun
YH
Magnetic Resonance Team, Korea Basic Science Institute, Ochang, Chungbuk 363-883, Korea.
Garron
Marie-Line
ML
Kim
Hye-Yeon
HY
Kim
Wan-Seok
WS
Zhang
Zhenqing
Z
Ryu
Kyeong-Seok
KS
Shaya
David
D
Xiao
Zhongping
Z
Cheong
Chaejoon
C
Kim
Yeong Shik
YS
Linhardt
Robert J
RJ
Jeon
Young Ho
YH
Cygler
Miroslaw
M
D001439:Bacteroides / Q000378:metabolism*; D002384:Catalysis; D003001:Cloning, Molecular; D004252:DNA Mutational Analysis; D006493:Heparin / Q000737:chemistry*; D019763:Heparin Lyase / Q000737:chemistry*; D007700:Kinetics; D008968:Molecular Conformation; D016297:Mutagenesis, Site-Directed; D011134:Polysaccharides / Q000737:chemistry; D011485:Protein Binding; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011994:Recombinant Proteins / Q000737:chemistry; D013379:Substrate Specificity
D011134:Polysaccharides; D011994:Recombinant Proteins; D006493:Heparin; D019763:Heparin Lyase