Structure-based clustering and mutagenesis of bacterial tannases reveals the importance and diversity of active site-capping domains

Journal article, 2024

Tannins are critical plant defense metabolites, enriched in bark and leaves, that protect against microorganisms and insects by binding to and precipitating proteins. Hydrolyzable tannins contain ester bonds which can be cleaved by tannases—serine hydrolases containing so-called “cap” domains covering their active sites. However, comprehensive insights into the biochemical properties and structural diversity of tannases are limited, especially regarding their cap domains. We here present a code pipeline for structure prediction-based hierarchical clustering to categorize the whole family of bacterial tannases, and have used it to discover new types of cap domains and other structural insertions among these enzymes. Subsequently, we used two recently identified tannases from the gut/soil bacterium Clostridium butyricum as model systems to explore the biochemical and structural properties of the cap domains of tannases. We demonstrate using molecular dynamics and mutagenesis that the cap domain covering the active site plays a major role in enzyme substrate preference, inhibition, and activity—despite not directly interacting with smaller substrates. The present work provides deeper knowledge into the mechanism, structural dynamics, and diversity of tannases. The structure-based clustering approach presents a new way of classifying any other enzyme family, and will be of relevance for enzyme types where activity is influenced by variable loop or insert regions appended to a core protein fold.