The interplay of descriptor-based computational analysis with pharmacophore modeling builds the basis for a novel classification scheme for feruloyl esterases

Abstract

One of the most intriguing groups of enzymes, the feruloyl esterases (FAEs), is ubiquitous in both simple and complex organisms. FAEs have gained importance in biofuel, medicine and food industries due to their capability of acting on a large range of substrates for cleaving ester bonds and synthesizing high-added value molecules through esterification and transesterification reactions. During the past two decades extensive studies have been carried out on the production and partial characterization of FAEs from fungi, while much less is known about FAEs of bacterial or plant origin. Initial classification studies on FAEs were restricted on sequence similarity and substrate specificity on just four model substrates and considered only a handful of FAEs belonging to the fungal kingdom. This study centers on the descriptor-based classification and structural analysis of experimentally verified and putative FAEs; nevertheless, the framework presented here is applicable to every poorly characterized enzyme family. 365 FAErelated sequences of fungal, bacterial and plantae origin were collected and they were clustered using

An unusual feruloyl esterase belonging to family VIII esterases and displaying a broad substrate range

“…There now exists a number of reports of CAZy enzymes possessing more than one catalytic domain: for example, an enzyme from Prevotella ruminicola 23 contains two carbohydrate esterase domains which separately confer acetyl-and ferulic esterase activities [53]. Another example, Clostridium thermocellum XynY [54], contains xylanase and feruloyl esterase domains (clustering with Type D FAEs) [45].…”

An enzyme from Auricularia auricula-judae combining both benzoyl and cinnamoyl esterase activity

“…The "nucleophilic elbow" consensus motif G-x-S-x-G (G-H-S-Y-G) around the active serine of the catalytic triad Ser174-His298-Asp333 was detected. Udatha et al [23] stated that the presence of the catalytic triad with the serine containing nucleophilic elbow was an essential criterion for being a putative FAE. The order of the predicted catalytic triad of FAEs was mostly characterized by Ser-Asp-His (77% out of 321 sequences), followed by Asp-Ser-His (12%) and His-Ser-Asp (11%) [23].…”

“…Udatha et al [23] stated that the presence of the catalytic triad with the serine containing nucleophilic elbow was an essential criterion for being a putative FAE. The order of the predicted catalytic triad of FAEs was mostly characterized by Ser-Asp-His (77% out of 321 sequences), followed by Asp-Ser-His (12%) and His-Ser-Asp (11%) [23]. The differing catalytic triad order Ser-His-Asp of EJD51015 as well as the missing homology to benzoyl esterases, FAEs and other enzymes confirmed EJD51015, and thus also EstBC to be a novel enzyme type.…”

A Chlorogenic Acid Esterase with a Unique Substrate Specificity from Ustilago maydis

“…3). Udatha et al (48) reported a catalytic triad of SerAsp-His for 324 analyzed feruloyl esterase sequences. Nonetheless, two feruloyl esterases containing a catalytic triad of Ser-GluHis (25,29) are also known.…”