Urbániková Ľubica
Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovak Republic.
3 Biotech. 2021 Feb;11(2):84. doi: 10.1007/s13205-020-02575-w. Epub 2021 Jan 19.
Bioinformatics analysis was focused on unique acetylesterases annotated in the CAZy database within the CE16 family and simultaneously belonging to the SGNH hydrolase superfamily. The CE16 acetylesterases were compared to structurally related SGNH hydrolases: (i) selected members of the CE2, CE3, CE6, CE12 and CE17 family of the CAZy database and (ii) structural representatives of the Lipase_GDSL and Lipase_GDSL_2 families according to the Pfam database. Sequence alignment based on four conserved sequence regions (CSRs) containing active-site residues was used to calculate sequence logos specific for each CE family and to construct a phylogenetic tree. In many members of the CE16 family, aspartic acid from the Ser-His-Asp catalytic triad has been replaced by asparagine, and based on structure-sequence comparison, an alternative catalytic dyad mechanism was predicted for these enzymes. In addition to four conserved regions, CSR-I, CSR-II, CSR-III and CSR-V, containing catalytic and oxyanion-hole residues, CSR-IV was found in the CE16 family as the only CAZy family. Tertiary structures of the characterized CE16 members prepared by homology modeling showed that the α/β/α sandwich fold as well as the topology of their active sites are preserved. The phylogenetic tree and sequence alignment indicate the existence of a subfamily in the CE16 family fully consistent with the known biochemical data. In addition, nonstandard CE16 members that differ from others were analyzed and their active-site residues were predicted. A better understanding of the structure-function relationship of acetylesterases can help in the targeted design of these enzymes for biotechnology.
The online version contains supplementary material available at 10.1007/s13205-020-02575-w.
生物信息学分析聚焦于碳水化合物活性酶数据库（CAZy）中CE16家族内注释的独特乙酰酯酶，且这些酶同时属于SGNH水解酶超家族。将CE16乙酰酯酶与结构相关的SGNH水解酶进行比较：（i）CAZy数据库中CE2、CE3、CE6、CE12和CE17家族的选定成员，以及（ii）根据Pfam数据库确定的脂肪酶_GDSL和脂肪酶_GDSL_2家族的结构代表。基于包含活性位点残基的四个保守序列区域（CSR）进行序列比对，以计算每个CE家族特有的序列标识并构建系统发育树。在CE16家族的许多成员中，丝氨酸-组氨酸-天冬氨酸催化三联体中的天冬氨酸已被天冬酰胺取代，基于结构-序列比较，预测这些酶存在另一种催化二元机制。除了包含催化和氧负离子洞残基的四个保守区域CSR-I、CSR-II、CSR-III和CSR-V外，CSR-IV在CE16家族中被发现是唯一的CAZy家族。通过同源建模制备的已表征CE16成员的三级结构表明，α/β/α三明治折叠及其活性位点的拓扑结构得以保留。系统发育树和序列比对表明，CE16家族中存在一个亚家族，这与已知的生化数据完全一致。此外，还分析了与其他成员不同的非标准CE16成员，并预测了它们的活性位点残基。更好地理解乙酰酯酶的结构-功能关系有助于针对生物技术对这些酶进行定向设计。
在线版本包含可在10.1007/s13205-020-02575-w获取的补充材料。
