Investigating the binding of beta-1,4-galactan to Bacillus licheniformis beta-1,4-galactanase by crystallography and computational modeling.

Jérôme Le Nours, Leonardo De Maria, Ditte Welner, Christel T Jørgensen, Lars L H Christensen, Torben V Borchert, Sine Larsen, Leila Lo Leggio

Biophysical Chemistry Group, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark.

Proteins 2009 Jun

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Microbial beta-1,4-galactanases are glycoside hydrolases belonging to family 53, which degrade galactan and arabinogalactan side chains in the hairy regions of pectin, a major plant cell wall component. They belong to the larger clan GH-A of glycoside hydrolases, which cover many different poly- and oligosaccharidase specificities. Crystallographic complexes of Bacillus licheniformis beta-1,4-galactanase and its inactive nucleophile mutant have been obtained with methyl-beta(1-->4)-galactotetraoside, providing, for the first time, information on substrate binding to the aglycone side of the beta-1,4-galactanase substrate binding groove. Using the experimentally determined subsites as a starting point, a beta(1-->4)-galactononaose was built into the structure and subjected to molecular dynamics simulations giving further insight into the residues involved in the binding of the polysaccharide from subsite -4 to +5. In particular, this analysis newly identified a conserved beta-turn, which contributes to subsites -2 to +3. This beta-turn is unique to family 53 beta-1,4-galactanases among all clan GH-A families that have been structurally characterized and thus might be a structural signature for endo-beta-1,4-galactanase specificity. Copyright 2008 Wiley-Liss, Inc.

Citation

Jérôme Le Nours, Leonardo De Maria, Ditte Welner, Christel T Jørgensen, Lars L H Christensen, Torben V Borchert, Sine Larsen, Leila Lo Leggio. Investigating the binding of beta-1,4-galactan to Bacillus licheniformis beta-1,4-galactanase by crystallography and computational modeling. Proteins. 2009 Jun;75(4):977-89