Alpha/beta-hydrolases: A unique structural motif coordinates catalytic acid residue in 40 protein fold families
Alpha/beta-hydrolases: A unique structural motif coordinates catalytic acid residue in 40 protein fold families
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DOI：
10.1002/prot.25338
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发表时间：
2017-10-01
影响因子：
2.9
通讯作者：
Denessiouk, Konstantin
中科院分区：
文献类型：
--
作者：
Dimitriou, Polytimi S.;Denesyuk, Alexander;Denessiouk, Konstantin
α/β-水解酶是具有共同折叠的酸-碱-亲核催化三联体酶家族，但使用多种底物，具有不同的最适pH，催化独特的催化反应，并且通常显示出改善的化学和热稳定性。ABH酶是蛋白质工程的主要目标。在这里，我们已经从40个结构ABH折叠家族的51个代表性成员中将活性位点分类为8个不同的保守几何形状。我们证明了发生一个共同的结构图案，催化酸区，在催化三元酸转。我们表明，外部配体的结合不改变催化酸区的结构，并且蛋白质的无配体和配体结合形式属于相同的催化酸区亚组。我们还表明，催化酸区协调的催化组氨酸环的位置直接在其平面上方，因此，固定在催化酸附近的适当位置的催化组氨酸。最后，我们证明了催化酸区在ABH酶的多亚基复合物形成中起着关键作用，并且参与与其他蛋白质的相互作用。因此，我们推测每个催化三联体残基都有自己的支持结构支架，类似于上述的催化酸区，它们共同形成了延伸的催化三联体基序。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突变，甚至可以补偿蛋白质功能的丧失。
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.