Glycosidases: Functions, Families and Folds

Abstract

Glycosidases catalyse the hydrolysis of glycosidic linkages, thereby degrading oligosaccharides and glycoconjugates, the structurally most diverse class of biopolymers. These efficient and highly specific catalysts play important roles in biological processes thus a detailed knowledge of glycosidase function is invaluable for understanding and controlling diseases and for industrial applications. The classification of this huge class of enzymes into families on the basis of amino acid sequence has provided a highly valuable tool for the analysis of structure‚Äďfunction relationships. Furthermore, the steady increase in three‚Äźdimensional structural information is revealing further evolutionary relationships between glycosidase families. In addition to the majority of glycosidases that act via the classical Koshland mechanisms, a growing number of such enzymes that use unusual mechanisms are being uncovered. This confluence of bioinformatics, structural and mechanistic studies has greatly advanced glycosidase engineering and the development of specific glycosidase inhibitors.

Key Concepts:

  • Classification of glycosidases by sequence similarity in a comprehensive database CAZy has proven to be an invaluable tool to analyse their structures and functions.

  • Glycosidases adopt a variety of folds.

  • The vast majority of glycosidases act via Koshland mechanisms with either retention or inversion of the anomeric configuration.

  • Some glycosidases use unusual mechanisms employing hydration, elimination and/or redox steps.

  • Detailed mechanistic understanding of glycosidase mechanism has allowed the engineering of glycosynthases and the development of specific inhibitors.

Keywords: glycosidase; carbohydrate; glycoconjugate; enzyme; hydrolysis; mechanism; catalysis; hydrolase

Figure 1.

Glycosidase folds: (a) (β/α)8 barrel, (b) jelly roll, (c) five fold propeller, (d) six fold propeller, (e) seven fold propeller, (f) (α/α)6 barrel, (g) (α/α)7 barrel, (h) right‐handed β‐helix, (i) dehydrogenase‐like fold and (j) lysozyme‐like fold.

Figure 2.

Active site topologies of saccharide‐degrading enzymes: (a) pocket, (b) cleft, (c) tunnel and (d) surface. The position of the catalytic residues is shown in red.

Figure 3.

Koshland mechanisms of glycoside hydrolysis by glycosidases (R1=sugar, R2=H), transglycosylases (R1 and R2=sugars) and glycosidase‐like phosphorylases (R1=sugar, R2=PO32−): (a) inverting α‐glycosidase, (b) inverting β‐glycosidase, (c) retaining α‐glycosidase, (d) retaining β‐glycosidase, (e) retaining N‐acetyl β‐hexosaminidase and (f) family 31 α‐glycan lyase (note that the covalent intermediate forms according to a Koshland mechanism, but breaks down by elimination, see also Fig ).

Figure 4.

Degradation of glycosides by elimination mechanisms: (a) family GH4 NAD+‐dependent glycoside hydrolases, (b) polysaccharide lyases (PL) and (c) unsaturated glucuronyl and galacturonyl hydrolases.

Figure 5.

Mechanisms of glycoside formation by engineered glycosidases: (a) glycosynthase, (b) thioglycoligase and (c) thioglycosynthase.

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Kötzler, Miriam P, Hancock, Susan M, and Withers, Stephen G(Jul 2014) Glycosidases: Functions, Families and Folds. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0020548.pub2]