1of1

File:1of1.jpg

spinqualitylabelsall models 1of1, resolution 1.95Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D

KINETICS AND CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS TYPE 1 THYMIDINE KINASE INTERACTING WITH (SOUTH)-METHANOCARBA-THYMIDINE

Overview

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.

About this Structure

1OF1 is a Single protein structure of sequence from Human herpesvirus 4 with SO4 and SCT as ligands. Active as Thymidine kinase, with EC number 2.7.1.21 Known structural/functional Site: AC1. Full crystallographic information is available from OCA.

Reference

The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery., Michel G, Pojasek K, Li Y, Sulea T, Linhardt RJ, Raman R, Prabhakar V, Sasisekharan R, Cygler M, J Biol Chem. 2004 Jul 30;279(31):32882-96. Epub 2004 May 21. PMID:15155751

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