Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5)

TLDR

The Glycoside Hydrolase family 5 (GH5) comprises a vast array of enzymes acting on β‑linked oligo‑ and polysaccharides from diverse organisms, yet its long, complex evolution and broad sequence diversity hinder functional prediction. The authors aimed to enhance differentiation of enzyme specificities and gain evolutionary insights by developing a new, robust subfamily classification of GH5. They achieved this by constructing a comprehensive subfamily framework that assigns GH5 sequences to distinct evolutionary groups. The study assigned roughly 80 % of GH5 sequences to 51 subfamilies, found that one‑third of catalytically active subfamilies are monospecific, identified 20 uncharacterized subfamilies, mapped functional knowledge onto a phylogenetic tree revealing uneven dispersion, and uncovered catalytically inactive proteins hinting at novel functions, thereby providing a curated resource for glycogenomics available at CAZy.

Abstract

Abstract Background The large Glycoside Hydrolase family 5 (GH5) groups together a wide range of enzymes acting on β-linked oligo- and polysaccharides, and glycoconjugates from a large spectrum of organisms. The long and complex evolution of this family of enzymes and its broad sequence diversity limits functional prediction. With the objective of improving the differentiation of enzyme specificities in a knowledge-based context, and to obtain new evolutionary insights, we present here a new, robust subfamily classification of family GH5. Results About 80% of the current sequences were assigned into 51 subfamilies in a global analysis of all publicly available GH5 sequences and associated biochemical data. Examination of subfamilies with catalytically-active members revealed that one third are monospecific (containing a single enzyme activity), although new functions may be discovered with biochemical characterization in the future. Furthermore, twenty subfamilies presently have no characterization whatsoever and many others have only limited structural and biochemical data. Mapping of functional knowledge onto the GH5 phylogenetic tree revealed that the sequence space of this historical and industrially important family is far from well dispersed, highlighting targets in need of further study. The analysis also uncovered a number of GH5 proteins which have lost their catalytic machinery, indicating evolution towards novel functions. Conclusion Overall, the subfamily division of GH5 provides an actively curated resource for large-scale protein sequence annotation for glycogenomics; the subfamily assignments are openly accessible via the Carbohydrate-Active Enzyme database at http://www.cazy.org/GH5.html .