Structural Comparison and Simulation of Pneumococcal Peptidoglycan Hydrolase LytB.
Structural Comparison and Simulation of Pneumococcal Peptidoglycan Hydrolase LytB.
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DOI：
10.1007/978-1-4939-3676-2_19
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发表时间：
2016
影响因子：
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通讯作者：
X. Bai;Qiong Li;Yong-Liang Jiang;Jing-Ren Zhang;Yuxing Chen;Cong-Zhao Zhou
中科院分区：
文献类型：
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作者：
X. Bai;Qiong Li;Yong-Liang Jiang;Jing-Ren Zhang;Yuxing Chen;Cong-Zhao Zhou
三维结构测定结合与同源物的全面比较是破译酶分子功能的简单策略。然而，在许多情况下，很难获得具有底物/配体的复合物结构。基于结构的分子模拟提供了一种替代的解决方案来预测底物/配体与酶的结合模式。肺炎链球菌（Streptococcus pneumoniae）LytB是一种肽聚糖水解酶，能裂解糖苷键，参与细胞分裂，但其催化机制尚不清楚。基于LytB的催化结构域（称为LytBCAT）的晶体结构，我们在这里描述如何分配三个LytBCAT模块的分子功能：SH 3b，WW和GH 73，使用结构比较。此外，我们对接到LytBCAT上的肽聚糖的推定的四肽-五肽底物提供底物结合模式的细节。四肽-五肽很好地容纳在由三个模块形成的T形底物结合口袋中。结合定点突变的水解活性测定进一步证实了结构比较和模拟所得出的结论。
Three-dimensional structural determination combined with comprehensive comparisons with the homologs is a straightforward strategy to decipher the molecular function of an enzyme. However, in many cases it’s difficult to obtain the complex structure with the substrate/ligand. Structure-based molecular simulation provides an alternative solution to predict the binding pattern of a substrate/ligand to the enzyme. TheStreptococcus pneumoniaeLytB is a peptidoglycan hydrolase that cleaves the glycosidic bond and therefore involves the cell division; however, the details of catalytic mechanism remain unknown. Based on the crystal structure of the catalytic domain of LytB (termed LytBCAT), we describe here how to assign the molecular functions of three LytBCATmodules: SH3b, WW, and GH73, using structural comparisons. Moreover, we dock a putative tetrasaccharide-pentapeptide substrate of peptidoglycan onto LytBCATto provide the details of substrate binding pattern. The tetrasaccharide-pentapeptide is well accommodated in a T-shaped substrate binding pocket formed by the three modules. The conclusions deduced from structural comparison and simulation are further proved by the hydrolytic activity assays in combination with site-directed mutagenesis.