The active site of the SGNH hydrolase-like fold proteins: Nucleophile–oxyanion (Nuc-Oxy) and Acid–Base zones

IF 2.7 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Current Research in Structural Biology Pub Date : 2024-01-01 DOI:10.1016/j.crstbi.2023.100123

Konstantin Denessiouk , Alexander I. Denesyuk , Sergei E. Permyakov , Eugene A. Permyakov , Mark S. Johnson , Vladimir N. Uversky

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Abstract

SGNH hydrolase-like fold proteins are serine proteases with the default Asp-His-Ser catalytic triad. Here, we show that these proteins share two unique conserved structural organizations around the active site: (1) the Nuc-Oxy Zone around the catalytic nucleophile and the oxyanion hole, and (2) the Acid-Base Zone around the catalytic acid and base. The Nuc-Oxy Zone consists of 14 amino acids cross-linked with eight conserved intra- and inter-block hydrogen bonds. The Acid–Base Zone is constructed from a single fragment of the polypeptide chain, which incorporates both the catalytic acid and base, and whose N- and C-terminal residues are linked together by a conserved hydrogen bond. The Nuc-Oxy and Acid-Base Zones are connected by an SHLink, a two-bond conserved interaction from amino acids, adjacent to the catalytic nucleophile and base.

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SGNH 水解酶样折叠蛋白的活性位点：亲核-亲氧（Nuc-Oxy）区和酸碱区

SGNH 水解酶样折叠蛋白是丝氨酸蛋白酶，具有默认的 Asp-His-Ser 催化三元组。在这里，我们展示了这些蛋白质在活性位点周围共享两种独特的保守结构组织：（1）围绕催化亲核体和氧阴离子孔的 Nuc-Oxy 区，以及（2）围绕催化酸和碱的 Acid-Base 区。核氧基区由 14 个氨基酸组成，通过 8 个保守的区块内和区块间氢键交联。酸碱区由多肽链的一个片段构成，其中包含催化酸和碱，其 N 端和 C 端残基通过一个保守的氢键连接在一起。亲核酸区和酸碱区通过 SHLink 连接在一起，SHLink 是氨基酸之间的一种双键保守相互作用，与催化亲核酸和碱相邻。

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