Multitasking in the gut: the X-ray structure of the multidomain BbgIII from Bifidobacterium bifidum offers possible explanations for its alternative functions,Acta Crystallographica Section D

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Multitasking in the gut: the X-ray structure of the multidomain BbgIII from Bifidobacterium bifidum offers possible explanations for its alternative functions
Acta Crystallographica Section D ( IF 2.6 ) Pub Date : 2021-11-18 , DOI: 10.1107/s2059798321010949
Olga V Moroz ₁ , Elena Blagova ₁ , Andrey A Lebedev ₂ , Filomeno Sánchez Rodríguez ₃ , Daniel J Rigden ₃ , Jeppe Wegener Tams ₄ , Reinhard Wilting ₄ , Jan Kjølhede Vester ₄ , Elena Longhin ₄ , Gustav Hammerich Hansen ₄ , Kristian Bertel Rømer Mørkeberg Krogh ₄ , Roland A Pache ₄ , Gideon J Davies ₁ , Keith S Wilson ₁

Affiliation

β-Galactosidases catalyse the hydrolysis of lactose into galactose and glucose; as an alternative reaction, some β-galactosidases also catalyse the formation of galactooligosaccharides by transglycosylation. Both reactions have industrial importance: lactose hydrolysis is used to produce lactose-free milk, while galactooligosaccharides have been shown to act as prebiotics. For some multi-domain β-galactosidases, the hydrolysis/transglycosylation ratio can be modified by the truncation of carbohydrate-binding modules. Here, an analysis of BbgIII, a multidomain β-galactosidase from Bifidobacterium bifidum, is presented. The X-ray structure has been determined of an intact protein corresponding to a gene construct of eight domains. The use of evolutionary covariance-based predictions made sequence docking in low-resolution areas of the model spectacularly easy, confirming the relevance of this rapidly developing deep-learning-based technique for model building. The structure revealed two alternative orientations of the CBM32 carbohydrate-binding module relative to the GH2 catalytic domain in the six crystallographically independent chains. In one orientation the CBM32 domain covers the entrance to the active site of the enzyme, while in the other orientation the active site is open, suggesting a possible mechanism for switching between the two activities of the enzyme, namely lactose hydrolysis and transgalactosylation. The location of the carbohydrate-binding site of the CBM32 domain on the opposite site of the module to where it comes into contact with the catalytic GH2 domain is consistent with its involvement in adherence to host cells. The role of the CBM32 domain in switching between hydrolysis and transglycosylation modes offers protein-engineering opportunities for selective β-galactosidase modification for industrial purposes in the future.

中文翻译：

肠道中的多任务处理：来自双歧杆菌的多域 BbgIII 的 X 射线结构为其替代功能提供了可能的解释

β-半乳糖苷酶催化乳糖水解成半乳糖和葡萄糖；作为替代反应，一些β-半乳糖苷酶还通过转糖基化催化低聚半乳糖的形成。这两种反应都具有工业重要性：乳糖水解用于生产无乳糖牛奶，而低聚半乳糖已被证明可作为益生元。对于一些多域 β-半乳糖苷酶，水解/转糖基化比率可以通过截断碳水化合物结合模块来修改。在这里，BbgIII 的分析，一种来自双歧杆菌的多域 β-半乳糖苷酶，被呈现。已经确定了对应于八个结构域的基因构建体的完整蛋白质的 X 射线结构。使用基于进化协方差的预测使模型的低分辨率区域中的序列对接变得非常容易，证实了这种快速发展的基于深度学习的模型构建技术的相关性。该结构揭示了 CBM32 碳水化合物结合模块相对于六个晶体学独立链中的 GH2 催化结构域的两个替代方向。在一个方向上，CBM32 结构域覆盖了酶活性位点的入口，而在另一个方向上，活性位点是开放的，这表明在酶的两种活性之间转换的可能机制，即乳糖水解和转半乳糖基化。CBM32 结构域的碳水化合物结合位点在模块与催化 GH2 结构域接触的相反位点上的位置与其参与宿主细胞的粘附一致。CBM32 结构域在水解和转糖基化模式之间切换中的作用为未来工业用途的选择性 β-半乳糖苷酶修饰提供了蛋白质工程机会。

更新日期：2021-12-06

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