2dt2

Crystal structure of the complex formed between goat signalling protein with pentasaccharide at 2.9A resolution

spinqualitylabelsall models 2dt2, resolution 2.90Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2dt2 is a 1 chain structure with sequence from Capra hircus. This structure supersedes the now removed PDB entries 2b40 and 2a0o. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: NAG Related: 2dpe, 2esc, 2dsz, 2dt0, 2dt1, 2dt3 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [CH3L1_CAPHI] Carbohydrate-binding lectin with a preference for chitin. May play a role in defense against pathogens, or in tissue remodeling. May play an important role in the capacity of cells to respond to and cope with changes in their environment. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed 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. 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Chitinase-3-like protein 3D structures

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