Dimitriou Polytimi S, Denesyuk Alexander, Takahashi Seiji, Yamashita Satoshi, Johnson Mark S, Nakayama Toru, Denessiouk Konstantin
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, Pushchino, 142290, Russia.
Proteins. 2017 Oct;85(10):1845-1855. doi: 10.1002/prot.25338. Epub 2017 Jul 3.
The alpha/beta-hydrolases are a family of acid-base-nucleophile catalytic triad enzymes with a common fold, but using a wide variety of substrates, having different pH optima, catalyzing unique catalytic reactions and often showing improved chemical and thermo stability. The ABH enzymes are prime targets for protein engineering. Here, we have classified active sites from 51 representative members of 40 structural ABH fold families into eight distinct conserved geometries. We demonstrate the occurrence of a common structural motif, the catalytic acid zone, at the catalytic triad acid turn. We show that binding of an external ligand does not change the structure of the catalytic acid zone and both the ligand-free and ligand-bound forms of the protein belong to the same catalytic acid zone subgroup. We also show that the catalytic acid zone coordinates the position of the catalytic histidine loop directly above its plane, and consequently, fixes the catalytic histidine in a proper position near the catalytic acid. Finally, we demonstrate that the catalytic acid zone plays a key role in multi-subunit complex formation in ABH enzymes, and is involved in interactions with other proteins. As a result, we speculate that each of the catalytic triad residues has its own supporting structural scaffold, similar to the catalytic acid zone, described above, which together form the extended catalytic triad motif. Each scaffold coordinates the function of its respective catalytic residue, and can even compensate for the loss of protein function, if the catalytic amino acid is mutated.
α/β水解酶是一类具有共同折叠结构的酸碱亲核催化三联体酶，但它们使用多种底物，具有不同的最适pH值，催化独特的催化反应，并且通常表现出更好的化学稳定性和热稳定性。ABH酶是蛋白质工程的主要目标。在这里，我们将40个具有结构ABH折叠家族的51个代表性成员的活性位点分类为八种不同的保守几何结构。我们证明了在催化三联体酸转角处存在一个共同的结构基序，即催化酸区。我们表明，外部配体的结合不会改变催化酸区的结构，并且蛋白质的无配体形式和配体结合形式都属于同一催化酸区亚组。我们还表明，催化酸区在其平面上方直接协调催化组氨酸环的位置，因此，将催化组氨酸固定在催化酸附近的适当位置。最后，我们证明催化酸区在ABH酶的多亚基复合物形成中起关键作用，并参与与其他蛋白质的相互作用。因此，我们推测催化三联体的每个残基都有其自己的支持性结构支架，类似于上述催化酸区，它们共同形成扩展的催化三联体基序。每个支架协调其各自催化残基的功能，并且如果催化氨基酸发生突变，甚至可以补偿蛋白质功能的丧失。
