Carbohydrate-active enzymes

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• Author: Stephen Withers
• Responsible Curator: Spencer Williams

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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 to 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 other, non-carbohydrate molecules to generate a wide range of glycoconjugates. Reflecting this structural diversity, there is a large diversity of enzymes involved in the biosynthesis, modification, binding and catabolism of carbohydrates.

The Carbohydrate Active EnZyme (CAZy) classification is a sequence-based classification of enzymes that are active on carbohydrate structures [1, 2, 3]. The creation of a family requires at least one biochemically-characterized member, and is based on the concept that sequence defines protein structure, and protein 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.

Glycoside hydrolases (GH)

Strictly speaking, the term 'glycoside hydrolase' or 'glycosidase' refers to enzymes that catalyze the hydrolytic cleavage of the glycosidic bond to give the carbohydrate hemiacetal. However, it is found that sequence-based classification methods often group in enzymes that have non-hydrolytic activities into the same families as hydrolytic enzymes.

• Transglycosidases: Sequence analysis groups transglycosidases with retaining glycoside hydrolases. According to all available evidencetransglycosidases and glycoside hydrolases use the same mechanism, except that a sugar or some other group, rather than water, acts as the nucleophile.

• Phosphorylases]]: Sequence similarly groups many, but all (see Glycosyltransferases, below) phosphorylases with retaining and inverting glycoside hydrolases. Enzymatic cleavage of the bond between two sugars or between a sugar and another group by reaction with phosphate is termed phosphorolysis, and yields the sugar-1-phosphate, and the reaction is reversible, allowing syntehsis of glycosidic linkages form sugar-1-phosphates. Again, GH-like phosphorylases share mechanistic similarities with glycoside hydrolases.

• Alpha-glucan lyases: An unusual group of enzymes has been found within family GH31 termed alpha-glucan lyases that degrade starch via an elimination mechanism, rather than via hydrolysis, forming an unsaturated (enol) product that tautomerises to its keto form, 1,5-anhydro fructose. Again, there are mechanistic similarities between [[alpha-glucan lyases and glycoside hydrolases.

• NAD-dependent glycoside hydrolases: Another unusual group of enzymes use an NAD-cofactor to hydrolyze through a mechanism involving a redox reaction. These enzymes are found within familes GH4 and GH109.

Key GH classification reviews (incl. GH4 enzymes and GH31 lyases): [4, 5, 6, 7, 8, 9]

Polysaccharide lyases (PL)

Polysaccharide lyases (PLs) cleave uronic acid-containing polysaccharides via a β-elimination mechanism to generate an unsaturated hexenuronic acid residue and a new reducing end at the point of cleavage. These enzymes are distinct from alpha-glucan lyases, which are classified within the GH modules, as described above.

Key PL classification reviews: [10, 11]

Auxiliary activities (AA)

The original CAZy classification scheme aimed to describe the families of enzymes that cleave or build complex carbohydrates and the associated carbohydrate binding modules. The discovery that members of families CBM33 and family GH61 are lytic polysaccharide monooxygenases (LPMO), gave impetus to a reclassification of these families into a new category, the "Auxiliary Activities" [12]. The auxiliary activities are familes of catalytic proteins that are potentially involved in plant cell degradation through an ability to help the original GH, PL and CE enzymes gain access to the carbohydrates comprising the plant cell wall. Currently, the AA families contain redox active enzymes.

Key AA classification review: [12]

Glycosyltransferases (GT)

The principal enzymes that catalyze glycoside synthesis are nucleotide phosphosugar-dependent glycosyltransferases.

Phosphorylases fall into two mechanistic classes: glycoside hydrolase-like and glycosyltransferase-like, and are likewise classified into GH or GT families by sequence comparisons. A second, very small, group of alpha-glucan lyases is found within GH Family 31 and follows a cationic glycoside-hydrolase-like mechanism.

Key GT review: [13, 14, 15]

References

1. Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (A BJ Classics review, online only). DOI: 10.1042/BJ20080382

2. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, and Henrissat B. (2009). The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 2009;37(Database issue):D233-8. DOI:10.1093/nar/gkn663 |
3. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, and Henrissat B. (2014). The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014;42(Database issue):D490-5. DOI:10.1093/nar/gkt1178 |
4. Henrissat B (1991). A classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem J. 1991;280 ( Pt 2)(Pt 2):309-16. DOI:10.1042/bj2800309 |
5. Henrissat B and Bairoch A. (1993). New families in the classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem J. 1993;293 ( Pt 3)(Pt 3):781-8. DOI:10.1042/bj2930781 |
6. Davies G and Henrissat B. (1995). Structures and mechanisms of glycosyl hydrolases. Structure. 1995;3(9):853-9. DOI:10.1016/S0969-2126(01)00220-9 |
7. Henrissat B and Bairoch A. (1996). Updating the sequence-based classification of glycosyl hydrolases. Biochem J. 1996;316 ( Pt 2)(Pt 2):695-6. DOI:10.1042/bj3160695 |
8. Vocadlo DJ and Davies GJ. (2008). Mechanistic insights into glycosidase chemistry. Curr Opin Chem Biol. 2008;12(5):539-55. DOI:10.1016/j.cbpa.2008.05.010 |
9. Yip VL and Withers SG. (2006). Breakdown of oligosaccharides by the process of elimination. Curr Opin Chem Biol. 2006;10(2):147-55. DOI:10.1016/j.cbpa.2006.02.005 |
10. Lombard V, Bernard T, Rancurel C, Brumer H, Coutinho PM, and Henrissat B. (2010). A hierarchical classification of polysaccharide lyases for glycogenomics. Biochem J. 2010;432(3):437-44. DOI:10.1042/BJ20101185 |
11. Garron ML and Cygler M. (2010). Structural and mechanistic classification of uronic acid-containing polysaccharide lyases. Glycobiology. 2010;20(12):1547-73. DOI:10.1093/glycob/cwq122 |
12. Levasseur A, Drula E, Lombard V, Coutinho PM, and Henrissat B. (2013). Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes. Biotechnol Biofuels. 2013;6(1):41. DOI:10.1186/1754-6834-6-41 |
12. Levasseur A, Drula E, Lombard V, Coutinho PM, and Henrissat B. (2013). Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes. Biotechnol Biofuels. 2013;6(1):41. DOI:10.1186/1754-6834-6-41 |
13. Campbell JA, Davies GJ, Bulone V, and Henrissat B. (1997). A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities. Biochem J. 1997;326 ( Pt 3)(Pt 3):929-39. DOI:10.1042/bj3260929u |
14. Coutinho PM, Deleury E, Davies GJ, and Henrissat B. (2003). An evolving hierarchical family classification for glycosyltransferases. J Mol Biol. 2003;328(2):307-17. DOI:10.1016/s0022-2836(03)00307-3 |
15. Lairson LL, Henrissat B, Davies GJ, and Withers SG. (2008). Glycosyltransferases: structures, functions, and mechanisms. Annu Rev Biochem. 2008;77:521-55. DOI:10.1146/annurev.biochem.76.061005.092322 |
16. Boraston AB, Bolam DN, Gilbert HJ, and Davies GJ. (2004). Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Biochem J. 2004;382(Pt 3):769-81. DOI:10.1042/BJ20040892 |
17. Shoseyov O, Shani Z, and Levy I. (2006). Carbohydrate binding modules: biochemical properties and novel applications. Microbiol Mol Biol Rev. 2006;70(2):283-95. DOI:10.1128/MMBR.00028-05 |
18. Hashimoto H (2006). Recent structural studies of carbohydrate-binding modules. Cell Mol Life Sci. 2006;63(24):2954-67. DOI:10.1007/s00018-006-6195-3 |
19. Guillén D, Sánchez S, and Rodríguez-Sanoja R. (2010). Carbohydrate-binding domains: multiplicity of biological roles. Appl Microbiol Biotechnol. 2010;85(5):1241-9. DOI:10.1007/s00253-009-2331-y |
20. Gilbert HJ, Knox JP, and Boraston AB. (2013). Advances in understanding the molecular basis of plant cell wall polysaccharide recognition by carbohydrate-binding modules. Curr Opin Struct Biol. 2013;23(5):669-77. DOI:10.1016/j.sbi.2013.05.005 |