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dc.rights.licenseCC BY — Creative Commons Attribution
dc.contributor.authorMichel, G.
dc.contributor.authorLi, Y.
dc.contributor.authorSulea, T.
dc.contributor.authorLinhardt, Robert J.
dc.contributor.authorCygler, M.
dc.date2004
dc.date.accessioned2022-06-21T20:13:20Z
dc.date.available2022-06-21T20:13:20Z
dc.date.issued2004
dc.identifier.citationThe structure of chondroitin B lyase complexed with glycosaminoglycan fragments unravels calcium-dependent catalytic machinery, G. Michel, Y. Li, T. Sulea, R. J. Linhardt, M. Cygler, Journal of Biological Chemistry, 279, 32882-32896, 2004.
dc.identifier.urihttps://hdl.handle.net/20.500.13015/5114
dc.identifier.urihttps://doi.org/10.1074/jbc.M403421200
dc.descriptionJournal of Biological Chemistry, 279, 32882-32896
dc.descriptionNote : if this item contains full text it may be a preprint, author manuscript, or a Gold OA copy that permits redistribution with a license such as CC BY. The final version is available through the publisher’s platform.
dc.description.abstractChondroitinase B from Pedobacter heparinus is the only known enzyme strictly specific for dermatan sulfate and is a widely used enzymatic tool for the structural characterization of glycosaminoglycans. This β-helical polysaccharide lyase belongs to family PL-6 and cleaves the β(1,4) linkage of dermatan sulfate in a random manner, yielding 4,5-unsaturated dermatan sulfate disaccharides as the product. The previously reported structure of its complex with a dermatan sulfate disaccharide product identified the -1 and -2 subsites of the catalytic groove. We present here the structure of chondroitinase B complexed with several dermatan sulfate and chondroitin sulfate oligosaccharides. In particular, the soaking of chondroitinase B crystals with a dermatan sulfate hexasaccharide results in a complex with two dermatan sulfate disaccharide reaction products, enabling the identification of the +2 and +1 subsites. Unexpectedly, this structure revealed the presence of a calcium ion coordinated by sequence-conserved acidic residues and by the carboxyl group of the l-iduronic acid at the +1 subsite. Kinetic and site-directed mutagenesis experiments have subsequently demonstrated that chondroitinase B absolutely requires calcium for its activity, indicating that the protein-Ca2+-oligosaccharide complex is functionally relevant. Modeling of an intact tetrasaccharide in the active site of chondroitinase B provided a better understanding of substrate specificity and the role of Ca2+ in enzymatic activity. Given these results, we propose that the Ca2+ ion neutralizes the carboxyl moiety of the l-iduronic acid at the cleavage site, whereas the conserved residues Lys-250 and Arg-271 act as Brønsted base and acid, respectively, in the lytic degradation of dermatan sulfate by chondroitinase B.
dc.languageen_US
dc.language.isoENG
dc.publisherElsevier
dc.relation.ispartofThe Linhardt Research Labs Online Collection
dc.relation.ispartofRensselaer Polytechnic Institute, Troy, NY
dc.relation.urihttps://harc.rpi.edu/
dc.rightsAttribution 3.0 United States*
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/us/*
dc.subjectBiology
dc.subjectChemistry and chemical biology
dc.subjectChemical and biological engineering
dc.subjectBiomedical engineering
dc.titleThe structure of chondroitin B lyase complexed with glycosaminoglycan fragments unravels calcium-dependent catalytic machineryen_US
dc.typeArticle
dcterms.accessRightsOpen Access
dcterms.accessRightsA full text version is available in DSpace@RPI
dcterms.isVersionOfhttps://doi.org/10.1074/jbc.M403421200
dc.rights.holderCC BY : this license allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use. Credit must be given to the authors and the original work must be properly cited.
dc.creator.identifierhttps://orcid.org/0000-0003-2219-5833
dc.relation.departmentThe Linhardt Research Labs.
dc.relation.departmentThe Shirley Ann Jackson, Ph.D. Center for Biotechnology and Interdisciplinary Studies (CBIS)


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Except where otherwise noted, this item's license is described as CC BY — Creative Commons Attribution