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Oligosaccharide binding in family 8 glycosidases:  crystal structures of active-site mutants of the β-1,4-xylanase pXyl from Pseudoaltermonas haloplanktis TAH3a in complex with substrate and product
De Vos, D.; Collins, T.; Nerinckx, W.; Savvides, S.N.; Claeyssens, M.; Gerday, C.; Feller, G.; Van Beeumen, J. (2006). Oligosaccharide binding in family 8 glycosidases:  crystal structures of active-site mutants of the β-1,4-xylanase pXyl from Pseudoaltermonas haloplanktis TAH3a in complex with substrate and product. Biochemistry (Wash.) 45(15): 4797-4807. dx.doi.org/10.1021/bi052193e
In: Biochemistry (Washington). American Chemical Society: Easton, Pa.. ISSN 0006-2960, more
Peer reviewed article  

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Keyword
    Marine

Authors  Top 
  • De Vos, D.
  • Collins, T.
  • Nerinckx, W.
  • Savvides, S.N.
  • Claeyssens, M.
  • Gerday, C., more
  • Feller, G., more
  • Van Beeumen, J., more

Abstract
    The structures of inactive mutants D144A and E78Q of the glycoside hydrolase family 8 (GH-8) endo-β-1,4-d-xylanase (pXyl) from the Antarctic bacterium Pseudoalteromonas haloplanktis TAH3a in complex with its substrate xylopentaose (at 1.95 Å resolution) and product xylotriose (at 1.9 Å resolution) have been determined by X-ray crystallography. A detailed comparative analysis of these with the apo-enzyme and with other GH-8 structures indicates an induced fit mechanism upon ligand binding whereby a number of conformational changes and, in particular, a repositioning of the proton donor into a more catalytically competent position occurs. This has also allowed for the description of protein−ligand interactions in this enzyme and for the demarcation of subsites −3 to +3. An in-depth analysis of each of these subsites gives an insight into the structure−function relationship of this enzyme and the basis of xylose/glucose discrimination in family 8 glycoside hydrolases. Furthermore, the structure of the −1/+1 subsite spanning complex reveals that the substrate is distorted from its ground state conformation. Indeed, structural analysis and in silico docking studies indicate that substrate hydrolysis in GH-8 members is preceded by a conformational change, away from the substrate ground-state chair conformation, to a pretransition state local minimum 2SO conformation.

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