Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow region 142290, Russia; Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku 20520, Finland.
Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow region 142290, Russia.
Int J Biol Macromol. 2021 May 15;179:601-609. doi: 10.1016/j.ijbiomac.2021.03.042. Epub 2021 Mar 10.
Proteinases with the (chymo)trypsin-like serine/cysteine fold comprise a large superfamily performing their function through the Acid - Base - Nucleophile catalytic triad. In our previous work (Denesyuk AI, Johnson MS, Salo-Ahen OMH, Uversky VN, Denessiouk K. Int J Biol Macromol. 2020;153:399-411), we described a universal three-dimensional (3D) structural motif, NBCZone, that contains eleven amino acids: dipeptide 42 T-43 T, pentapeptide 54 T-55 T-56 T-57 T(base)-58 T, tripeptide 195 T(nucleophile)-196 T-197 T and residue 213 T (T - numeration of amino acids in trypsin). The comparison of the NBCZones among the members of the (chymo)trypsin-like protease family suggested the existence of 15 distinct groups. Within each group, the NBCZones incorporate an identical set of conserved interactions and bonds. In the present work, the structural environment of the catalytic acid at the position 102 T and the fourth member of the "catalytic tetrad" at the position 214 T was analyzed in 169 3D structures of proteinases with the (chymo)trypsin-like serine/cysteine fold. We have identified a complete Structural Catalytic Core (SCC) consisting of two classes and four groups. The proteinases belonging to different classes and groups differ from each other by the nature of the interaction between their N- and C-terminal β-barrels. Comparative analysis of the 3CLpro(s) from SARS-CoV-2 and SARS-CoV, used as an example, showed that the amino acids at positions 103 T and 179 T affect the nature of the interaction of the "catalytic acid" core (102 T-Core, N-terminal β-barrel) with the "supplementary" core (S-Core, C-terminal β-barrel), which ultimately results in the modulation of the enzymatic activity. The reported analysis represents an important standalone contribution to the analysis and systematization of the 3D structures of (chymo)trypsin-like serine/cysteine fold proteinases. The use of the developed approach for the comparison of 3D structures will allow, in the event of the appearance of new representatives of a given fold in the PDB, to quickly determine their structural homologues with the identification of possible differences.
具有糜蛋白酶样丝氨酸/半胱氨酸折叠的蛋白酶构成了一个庞大的超家族，通过酸-碱-亲核催化剂三联体发挥其功能。在我们之前的工作中（Denesyuk AI、Johnson MS、Salo-Ahen OMH、Uversky VN、Denessiouk K. Int J Biol Macromol. 2020;153:399-411），我们描述了一个通用的三维（3D）结构基序 NBCZone，它包含 11 个氨基酸：二肽 42T-43T、五肽 54T-55T-56T-57T(base)-58T、三肽 195T(nucleophile)-196T-197T 和残基 213T（T-编号在糜蛋白酶中的氨基酸）。对糜蛋白酶样蛋白酶家族成员的 NBCZones 进行比较表明，存在 15 个不同的组。在每个组中，NBCZones 都包含一组相同的保守相互作用和键。在本工作中，分析了具有糜蛋白酶样丝氨酸/半胱氨酸折叠的 169 种蛋白水解酶的 3D 结构中位置 102T 的催化酸和位置 214T 的“催化四联体”的第四个成员的结构环境。我们已经确定了一个完整的结构催化核心（SCC），由两类和四组组成。属于不同类和组的蛋白水解酶通过它们的 N-和 C-末端β-桶之间的相互作用的性质而彼此不同。以 SARS-CoV-2 和 SARS-CoV 的 3CLpro(s)为例的比较分析表明，位置 103T 和 179T 的氨基酸影响“催化酸”核心（102T-Core，N-末端β-桶）与“补充”核心（S-Core，C-末端β-桶）之间相互作用的性质，这最终导致酶活性的调节。所报道的分析是对糜蛋白酶样丝氨酸/半胱氨酸折叠蛋白水解酶的 3D 结构分析和系统化的重要独立贡献。使用所开发的方法进行 3D 结构比较，将允许在给定折叠的新代表出现在 PDB 中时，快速确定它们的结构同源物，并识别可能的差异。
