Abstract
BackgroundThe 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.ResultsAbout 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.ConclusionOverall, 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.
Highlights
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
Naming follows the procedure devised for GH13, where the family number is followed by an Arabic numeral that reflects the order of creation [24]: GH5_1 to GH5_53
One aim of the present investigation was to obtain an improved correlation between protein sequences and catalytic specificity by refining a finer hierarchical level, the subfamily, for GH5 members
Summary
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. 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. Carbohydrates, in the form of mono-, di-, oligo-, and polysaccharides, as well as glycoconjugates, play fundamental roles in all forms of life [1]. Beyond their role in energy storage, carbohydrates are central to diverse biological processes such as host-pathogen interactions, signal transduction, inflammation, intracellular trafficking, diseases, and differentiation/development. A decade of investments in genomics and proteomics has greatly improved our interpretation of the molecular language of the cell, but deciphering the complex carbohydrate-based information in the biomolecular landscape is still in its infancy. Glycomics has been identified both as “the last frontier of molecular and cellular biology” [4] as well as an “emerging technology that will change the world” [5]
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