2B4F

Structure Of A Cold-Adapted Family 8 Xylanase in complex with substrate

Summary for 2B4F

• Entry DOI: 10.2210/pdb2b4f/pdb
• Related: 1H12 1H13 1H14
• Descriptor: endo-1,4-beta-xylanase, beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose (3 entities in total)
• Functional Keywords: hydrolase, xylan degradation, psychrophilic, cold adaptation, temperature, glycosyl hydrolase, family 8
• Biological source: Pseudoalteromonas haloplanktis
• Total number of polymer chains: 1
• Total formula weight: 47337.94

Authors

De Vos, D.,Collins, T.,Savvides, S.N.,Feller, G.,Van Beeumen, J.J. (deposition date: 2005-09-23, release date: 2006-09-05, Last modification date: 2024-10-30)

Primary citation

De Vos, D.,Collins, T.,Nerinckx, W.,Savvides, S.N.,Claeyssens, M.,Gerday, C.,Feller, G.,Van Beeumen, J.
Oligosaccharide binding in family 8 glycosidases: crystal structures of active-site mutants of the beta-1,4-xylanase pXyl from Pseudoaltermonas haloplanktis TAH3a in complex with substrate and product.
Biochemistry, 45:4797-4807, 2006

PubMed Abstract: The structures of inactive mutants D144A and E78Q of the glycoside hydrolase family 8 (GH-8) endo-beta-1,4-d-xylanase (pXyl) from the Antarctic bacterium Pseudoalteromonas haloplanktis TAH3a in complex with its substrate xylopentaose (at 1.95 A resolution) and product xylotriose (at 1.9 A 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 (2)S(O) conformation.

PubMed: 16605248
DOI: 10.1021/bi052193e

Experimental method

X-RAY DIFFRACTION (1.95 Å)