Le Nours Jérôme, De Maria Leonardo, Welner Ditte, Jørgensen Christel T, Christensen Lars L H, Borchert Torben V, Larsen Sine, Lo Leggio Leila
Biophysical Chemistry Group, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark.
Proteins. 2009 Jun;75(4):977-89. doi: 10.1002/prot.22310.
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.
微生物β-1,4-半乳聚糖酶是属于第53家族的糖苷水解酶，可降解果胶（一种主要的植物细胞壁成分）毛状区域中的半乳聚糖和阿拉伯半乳聚糖侧链。它们属于糖苷水解酶中较大的GH-A家族，该家族涵盖许多不同的多糖和寡糖酶特异性。已获得地衣芽孢杆菌β-1,4-半乳聚糖酶及其无活性亲核突变体与甲基-β(1→4)-半乳糖四糖的晶体复合物，首次提供了关于底物与β-1,4-半乳聚糖酶底物结合凹槽糖苷配基侧结合的信息。以实验确定的亚位点为起点，将β(1→4)-半乳糖九糖构建到结构中，并进行分子动力学模拟，从而进一步深入了解参与多糖从亚位点-4到+5结合的残基。特别是，该分析新发现了一个保守的β-转角，它对亚位点-2到+3有贡献。在所有已进行结构表征的GH-A家族中，这个β-转角是第53家族β-1,4-半乳聚糖酶所特有的，因此可能是内切β-1,4-半乳聚糖酶特异性的结构特征。
