1of1: Difference between revisions

Chondroitinase 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, beta-helical polysaccharide lyase belongs to family PL-6 and cleaves the, beta(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-Ca(2+)-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, Ca(2+) in enzymatic activity. Given these results, we propose that the, Ca(2+) 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, Bronsted base and acid, respectively, in the lytic degradation of dermatan, sulfate by chondroitinase B.

1OF1 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Human_herpesvirus_4 Human herpesvirus 4] with SO4 and SCT as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Thymidine_kinase Thymidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.21 2.7.1.21] Structure known Active Site: AC1. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1OF1 OCA].  

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