2dt2
Crystal structure of the complex formed between goat signalling protein with pentasaccharide at 2.9A resolution
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OverviewOverview
A 40 kDa glycoprotein (SPG-40) secreted during involution works as a, protective signalling factor through its binding to viable cells. The, crystal structure of the native protein has been determined at 2.3 A, resolution. This is the first report on the carbohydrate-binding, properties of SPG-40; the structure determinations of the complexes of, SPG-40 with four oligosaccharides of different lengths at resolutions, ranging from 2.2 to 2.8 A are described. Carbohydrate-binding studies with, N-acetylglucosamines (GlcNAc(n), n = 3-6) using fluorescence spectroscopy, revealed poor binding effects with GlcNAc(3) and GlcNAc(4), while, GlcNAc(5) and GlcNAc(6) bound to SPG-40 with considerable strength; the, dissociation constants (K(d)) were estimated to be 260 +/- 3 and 18 +/- 4, microM, respectively. SPG-40 was cocrystallized with GlcNAc(3), GlcNAc(4), GlcNAc(5) and GlcNAc(6). The overall structure of native SPG-40 was, essentially similar to that reported previously at low resolution. The, structures of its complexes with GlcNAc(3), GlcNAc(4), GlcNAc(5) and, GlcNAc(6) revealed the positions of these oligosaccharides in the, carbohydrate-binding groove and provided insights into the mechanism of, binding of oligosaccharides to SPG-40, indicating that the preferred, subsites in the carbohydrate-binding groove of SPG-40 were from -4 to -2., The structure of the protein remained unperturbed upon binding of, GlcNAc(3) and GlcNAc(4), but the structure changed significantly upon, binding of GlcNAc(5) and GlcNAc(6). Significant conformational variations, were observed in the sugar-binding groove: Trp78 partially flipped out of, the barrel in GlcNAc(5), while in the GlcNAc(6) complex a completely, flipped-out Trp78 was observed along with several other conformational, changes, including those of Asp186 and Arg242. Such changes upon binding, to carbohydrates have not previously been observed in chitin-hydrolyzing, chitinases and reflect less favourable binding of carbohydrates to SPG-40., As this appears to essentially be a binding protein, this loss of binding, affinity might be compensated by other intermolecular interactions such as, protein-protein interactions and also by the binding of its own glycan, chain.
About this StructureAbout this Structure
2DT2 is a Single protein structure of sequence from Capra hircus. This structure superseeds the now removed PDB entries 2B40 and 2A0O. Full crystallographic information is available from OCA.
ReferenceReference
Carbohydrate-binding properties of goat secretory glycoprotein (SPG-40) and its functional implications: structures of the native glycoprotein and its four complexes with chitin-like oligosaccharides., Kumar J, Ethayathulla AS, Srivastava DB, Singh N, Sharma S, Kaur P, Srinivasan A, Singh TP, Acta Crystallogr D Biol Crystallogr. 2007 Apr;63(Pt 4):437-46. Epub 2007, Mar 16. PMID:17372347
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