Crystal structure of heparinase II from Pedobacter heparinus and its complex with a disaccharide product

From National Research Council Canada

DOIResolve DOI: https://doi.org/10.1074/jbc.M512055200
AuthorSearch for: ; Search for: 1; Search for: 1; Search for: ; Search for: ; Search for: ; Search for: 1
Name affiliation
  1. National Research Council of Canada. NRC Biotechnology Research Institute
FormatText, Article
Journal titleThe Journal of Biological Chemistry
ISSN0021-9258
1083-351X
Volume281
Issue22
Pages15525–15535
Subjectchondroitin ABC lyase; crystal structure; enzymes; heparin; lyase; mutation; pharmaceutical; protein
Abstract
Heparinase II depolymerizes heparin and heparan sulfate glycosaminoglycans, yielding unsaturated oligosaccharide products through an elimination degradation mechanism. This enzyme cleaves the oligosaccharide chain on the nonreducing end of either glucuronic or iduronic acid, sharing this characteristic with a chondroitin ABC lyase. We have determined the first structure of a heparin-degrading lyase, that of heparinase II from Pedobacter heparinus ( formerly Flavobacterium heparinum), in a ligand-free state at 2.15 (A) over circle resolution and in complex with a disaccharide product of heparin degradation at 2.30 (A) over circle resolution. The protein is composed of three domains: an N-terminal alpha-helical domain, a central two-layered beta-sheet domain, and a C-terminal domain forming a two-layered beta-sheet. Heparinase II shows overall structural similarities to the polysaccharide lyase family 8 ( PL8) enzymes chondroitin AC lyase and hyaluronate lyase. In contrast to PL8 enzymes, however, heparinase II forms stable dimers, with the two active sites formed independently within each monomer. The structure of the N- terminal domain of heparinase II is also similar to that of alginate lyases from the PL5 family. A Zn2+ ion is bound within the central domain and plays an essential structural role in the stabilization of a loop forming one wall of the substrate-binding site. The disaccharide binds in a long, deep canyon formed at the top of the N- terminal domain and by loops extending from the central domain. Based on structural comparison with the lyases from the PL5 and PL8 families having bound substrates or products, the disaccharide found in heparinase II occupies the '+1' and '+2' subsites. The structure of the enzyme -product complex, combined with data from previously characterized mutations, allows us to propose a putative chemical mechanism of heparin and heparan -sulfate degradation
Publication date
PublisherAmerican Society for Biochemistry and Molecular Biology
Note200626
LanguageEnglish
Peer reviewedYes
NRC numberNRC-BRI-47523
NPARC number3538995
Export citationExport as RIS
Report a correctionReport a correction
Record identifier18df9147-c387-4b8b-a553-70e10fe756b2
Record created2009-03-01
Record modified2020-04-22
Report a problem on this page
Date modified: