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Carbohydrate-active enzymes
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Carbohydrates collectively are an immensely important group of biomolecules. The individual monosaccharide units have the potential to be joined together to form oligo- and polysaccharides, with the glycosidic linkage occurring between the anomeric position of one sugar with the hydroxyl group of another. Owing ot the many hydroxy groups on each sugar, the potential for two possible anomeric configurations, and the possibility of different ring sizes (pyranose and furanose are the most common), there is a combinatorially-large number of structures possible. Further, carbohydrates can be linked to ther, non-carbohydrate molecules ot generate a wide range of glycoconjugates. Reflecting this structural diversity, there is a large diversity of enzymes involved in the biosynthesis, modification and catabolism of carbohydrates.
The Carbohydrate Active Enzyme classification is a sequence-based classificaiton of enzymes that are active on carbohydrate structures. The creation of a family requires at least one biochemically-characterized member, and is based on the concept that sequence defines structure, and structure defines function. Generally, but not exclusively, functional properties often extend to other members of the family, and provides a framework upon which to base testable hypotheses of enzyme structure and function.
The major classes of carbohydrate active enzymes within the CAZy classification are:
Glycoside hydrolases: Enzymatic formation and cleavage of the bond between two sugars or between a sugar and another group can occur by hydrolysis to give the free sugar (glycosidases or glycoside hydrolases), by transglycosylation to give a new glycoside (transglycosidases), by phosphorolysis to give the sugar-1-phosphate (phosphorylases) or by elimination to give unsaturated sugar products (lyases). The principal enzymes that catalyze glycoside synthesis are nucleotide phosphosugar-dependent glycosyltransferases.
Sequence analysis methods allow the grouping of proteins into sequence-related families. Sets of sequence-related enzymes are termed families. Sequence analysis groups transglycosidases with glycoside hydrolases (e.g. Glycoside Hydrolase Family 13 cyclodextrin glucanotransferases and amylases). According to all available evidence transglycosidases and glycoside hydrolases use the same mechanism, except that a sugar or some other group, rather than water, acts as the nucleophile.
Phosphorylases fall into two mechanistic classes: glycoside hydrolase-like and glycosyltransferase-like, and are likewise classified into GH or GT families by sequence comparisons. Lyases fall into two mechanistic classes. The largest class is that which cleaves polymers containing uronic acids: most commonly pectins and glycosaminoglycans. These enzymes break the bond between the glycosidic oxygen and the ring carbon of the sugar in the +1 site via an elimination mechanism. This is the group separately classified in CAZY as polysaccharide lyases (PLs). A second, very small, group of alpha-glucan lyases is found within GH Family 31 and follows a cationic glycoside-hydrolase-like mechanism.