Abstract
The alpha/beta-Hydrolases (ABH) are a structural class of proteins that are found widespread in nature and includes enzymes that can catalyze various reactions in different substrates. The catalytic versatility of the ABH fold enzymes, which has been a valuable property in protein engineering applications, is based on a similar acid-base-nucleophile catalytic mechanism. In our research, we are concerned with the structure that surrounds the key units of the catalytic machinery, and we have previously found conserved structural organizations that coordinate the catalytic acid, the catalytic nucleophile and the residues of the oxyanion hole. Here, we explore the architecture that surrounds the catalytic histidine at the active sites of enzymes from 40 ABH fold families, where we have identified six conserved interactions that coordinate the catalytic histidine next to the catalytic acid and the catalytic nucleophile. Specifically, the catalytic nucleophile is coordinated next to the catalytic histidine by two weak hydrogen bonds, while the catalytic acid is directly involved in the coordination of the catalytic histidine through by two weak hydrogen bonds. The imidazole ring of the catalytic histidine is coordinated by a CH-π contact and a hydrophobic interaction. Moreover, the catalytic triad residues are connected with a residue that is located at the core of the active site of ABH fold, which is suggested to be the fourth member of a “structural catalytic tetrad”. Besides their role in the stability of the catalytic mechanism, the conserved elements of the catalytic site are actively involved in ligand binding and affect other properties of the catalytic activity, such as substrate specificity, enantioselectivity, pH optimum and thermostability of ABH fold enzymes. These properties are regularly targeted in protein engineering applications, and thus, the identified conserved structural elements can serve as potential modification sites in order to develop ABH fold enzymes with altered activities.
Highlights
The structural family of alpha/beta-Hydrolases (ABH) includes enzymes that are widely found in nature and have diverse functions, such as esterases, lipases, thioesterases, amidases, epoxide hydrolases, dehalogenases, haloperoxidases, and hydroxynytrile lyases [1,2,3]
As we have reviewed in the Introduction section, the residues of the acid-base-nucleophile catalytic triad of the ABH fold enzymes are located at conserved positions across the ABH fold: the catalytic acid and the catalytic nucleophile are located at the same plane with the β-sheet, while the catalytic base, a conserved histidine, is located outside this plane, but directly interacts with the other two catalytic residues
In order to explore the coordination of the catalytic histidine relative to the catalytic nucleophile and the catalytic acid, our comparative analysis has been conducted in two parts: the first part is concerned with the structure around the catalytic nucleophile-base pair, and the second part is concerned with the structure that surrounds the catalytic acid-base pair
Summary
The structural family of alpha/beta-Hydrolases (ABH) includes enzymes that are widely found in nature and have diverse functions, such as esterases, lipases, thioesterases, amidases, epoxide hydrolases, dehalogenases, haloperoxidases, and hydroxynytrile lyases [1,2,3]. Because of their remarkable catalytic versatility, the ABH fold enzymes have often served as targets in protein engineering applications for the development of biocatalysts with improved characteristics [4]. Located opposite to the catalytic triad, the oxyanion hole is usually shaped by two residues, one of which follows the catalytic nucleophile and the second is located at the C-terminus of strand β3 [1, 6, 7]
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