2QZ3

Crystal structure of a glycoside hydrolase family 11 xylanase from Bacillus subtilis in complex with xylotetraose

Summary for 2QZ3

• Entry DOI: 10.2210/pdb2qz3/pdb
• Related PRD ID: PRD_900117
• Descriptor: Endo-1,4-beta-xylanase A, beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose, ACETIC ACID, ... (4 entities in total)
• Functional Keywords: glycoside hydrolase, xylanase, glycosidase, xylan degradation, hydrolase
• Biological source: Bacillus subtilis
• Total number of polymer chains: 2
• Total formula weight: 42391.38

Authors

Vandermarliere, E.,Bourgois, T.M.,Strelkov, S.V.,Delcour, J.A.,Courtin, C.M.,Rabijns, A. (deposition date: 2007-08-16, release date: 2007-12-11, Last modification date: 2023-10-25)

Primary citation

Vandermarliere, E.,Bourgois, T.M.,Rombouts, S.,Van Campenhout, S.,Volckaert, G.,Strelkov, S.V.,Delcour, J.A.,Rabijns, A.,Courtin, C.M.
Crystallographic analysis shows substrate binding at the -3 to +1 active-site subsites and at the surface of glycoside hydrolase family 11 endo-1,4-beta-xylanases.
Biochem.J., 410:71-79, 2008

PubMed Abstract: GH 11 (glycoside hydrolase family 11) xylanases are predominant enzymes in the hydrolysis of heteroxylan, an abundant structural polysaccharide in the plant cell wall. To gain more insight into the protein-ligand interactions of the glycone as well as the aglycone subsites of these enzymes, catalytically incompetent mutants of the Bacillus subtilis and Aspergillus niger xylanases were crystallized, soaked with xylo-oligosaccharides and subjected to X-ray analysis. For both xylanases, there was clear density for xylose residues in the -1 and -2 subsites. In addition, for the B. subtilis xylanase, there was also density for xylose residues in the -3 and +1 subsite showing the spanning of the -1/+1 subsites. These results, together with the observation that some residues in the aglycone subsites clearly adopt a different conformation upon substrate binding, allowed us to identify the residues important for substrate binding in the aglycone subsites. In addition to substrate binding in the active site of the enzymes, the existence of an unproductive second ligand-binding site located on the surface of both the B. subtilis and A. niger xylanases was observed. This extra binding site may have a function similar to the separate carbohydrate-binding modules of other glycoside hydrolase families.

PubMed: 17983355
DOI: 10.1042/BJ20071128

Experimental method

X-RAY DIFFRACTION (1.8 Å)