Identification of Three Conserved Interaction Zones Around the Catalytic Machinery of alpha/beta- Hydrolase Fold Enzymes
Dimitriou, Polytimi (2020-03-06)
Dimitriou, Polytimi
Åbo Akademi - Åbo Akademi University
06.03.2020
This publication is copyrighted. You may download, display and print it for Your own personal use. Commercial use is prohibited.
Publikationens permanenta adress är
https://urn.fi/URN:ISBN:978-952-12-3928-1
https://urn.fi/URN:ISBN:978-952-12-3928-1
Abstrakt
The alpha/beta-Hydrolases (ABH) comprise one of the largest structural families of proteins, found in all organisms. Although they share low sequence similarity, the ABH fold enzymes maintain a common catalytic domain, the ABH fold, and are capable of catalyzing various reactions on different substrates by using similar acid-base-nucleophile catalytic triad residues that are located at conserved positions across the catalytic subsite.
Due to their catalytic versatility, the ABH fold enzymes are actively investigated, and often serve as targets in protein engineering applications, which modify the ABH fold enzymes and customize their catalytic properties so that they are functional within the demanding and usually extreme conditions of industrial settings. Nevertheless, the inadequate understanding of the relationship between the structure and function of the ABH fold enzymes hinders their utilization in the development of biocatalysts with desired physical properties, altered catalytic activities and recognition of novel substrates. Even so, there are many successful experimental studies that have managed to tailor the catalytic activities of individual ABH fold enzymes, while pointing at structural elements of their active sites for influencing their catalytic activities.
Motivated by the findings of published experimental studies, this thesis has explored and analyzed the architecture of the active sites of representative structures from 40 ABH fold enzymes families, seeking to identify similarities and differences in the geometries of the catalytic subsites of the functionally unrelated ABH fold enzymes. Thus, this research has been a systematic and thorough analysis of the relationship between protein structure and function that is based on the structural features of ABH fold and is not concerned with the differences in the sequence and function of ABH fold enzymes.
This comprehensive analysis, which is focused on the geometry around the key units of the catalytic machinery, has shown that the catalytic acid, the catalytic base, the catalytic nucleophile and the residues that help form the oxyanion hole in ABH fold enzymes are coordinated by sets of conserved structural elements. Specifically, the catalytic acid, the catalytic nucleophile and the residues of the oxyanion zone are coordinated by planar, closed structural organizations that are termed the “catalytic acid zone”, the “nucleophile zone”, and the “oxyanion zone”, respectively; the catalytic base, which is a conserved histidine, is itself coordinated by set of distinct structural elements. These three zones and the structural elements associated with histidine are connected by a conserved hydrogen-bonding network that extends throughout the active site of ABH fold enzymes, here termed the conserved catalytic structural core. Altogether these structural components serve to optimally arrange the residues that comprise the catalytic machinery and secure the structural integrity of the active site of ABH fold enzymes.
Combined with information from the literature, it is shown that several of the conserved structural elements of the catalytic core are indispensable for the function of the ABH fold enzymes due to their critical structural role, while many of them are also able to affect catalytic properties such as the pH optimum, thermostability, substrate specificity and enantioselectivity, and contribute to other aspects of the enzymatic activity, including the oligomerization, the formation of protein-protein complexes, and ligand binding.
Overall, this research indicates that the function of the versatile ABH fold enzymes is largely associated with the robust infrastructure of the active site that is composed of conserved structural elements, and thus, these findings could find application in protein engineering tasks, whereby the identified structural elements can be considered as possible modification sites.
Due to their catalytic versatility, the ABH fold enzymes are actively investigated, and often serve as targets in protein engineering applications, which modify the ABH fold enzymes and customize their catalytic properties so that they are functional within the demanding and usually extreme conditions of industrial settings. Nevertheless, the inadequate understanding of the relationship between the structure and function of the ABH fold enzymes hinders their utilization in the development of biocatalysts with desired physical properties, altered catalytic activities and recognition of novel substrates. Even so, there are many successful experimental studies that have managed to tailor the catalytic activities of individual ABH fold enzymes, while pointing at structural elements of their active sites for influencing their catalytic activities.
Motivated by the findings of published experimental studies, this thesis has explored and analyzed the architecture of the active sites of representative structures from 40 ABH fold enzymes families, seeking to identify similarities and differences in the geometries of the catalytic subsites of the functionally unrelated ABH fold enzymes. Thus, this research has been a systematic and thorough analysis of the relationship between protein structure and function that is based on the structural features of ABH fold and is not concerned with the differences in the sequence and function of ABH fold enzymes.
This comprehensive analysis, which is focused on the geometry around the key units of the catalytic machinery, has shown that the catalytic acid, the catalytic base, the catalytic nucleophile and the residues that help form the oxyanion hole in ABH fold enzymes are coordinated by sets of conserved structural elements. Specifically, the catalytic acid, the catalytic nucleophile and the residues of the oxyanion zone are coordinated by planar, closed structural organizations that are termed the “catalytic acid zone”, the “nucleophile zone”, and the “oxyanion zone”, respectively; the catalytic base, which is a conserved histidine, is itself coordinated by set of distinct structural elements. These three zones and the structural elements associated with histidine are connected by a conserved hydrogen-bonding network that extends throughout the active site of ABH fold enzymes, here termed the conserved catalytic structural core. Altogether these structural components serve to optimally arrange the residues that comprise the catalytic machinery and secure the structural integrity of the active site of ABH fold enzymes.
Combined with information from the literature, it is shown that several of the conserved structural elements of the catalytic core are indispensable for the function of the ABH fold enzymes due to their critical structural role, while many of them are also able to affect catalytic properties such as the pH optimum, thermostability, substrate specificity and enantioselectivity, and contribute to other aspects of the enzymatic activity, including the oligomerization, the formation of protein-protein complexes, and ligand binding.
Overall, this research indicates that the function of the versatile ABH fold enzymes is largely associated with the robust infrastructure of the active site that is composed of conserved structural elements, and thus, these findings could find application in protein engineering tasks, whereby the identified structural elements can be considered as possible modification sites.