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Carbohydrate-active enzymes

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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 [1, 2]. 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 [3]. Further, carbohydrates can be linked to other, non-carbohydrate molecules to generate a wide range of glycoconjugates [4]. 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

The Carbohydrate Active EnZyme (CAZy) classification is a sequence-based classification of enzymes that synthesize or break-down saccharides, which originated with the seminal grouping of glycoside hydrolases by Bernard Henrissat ([5, 6, 7, 8]; see [9] for a lucid historical review). 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 [10]. Since its inception, the CAZy classification and associated database has undergone continually active curation, including the addition of new enzyme and associated module classes [11, 12]. Hence, the CAZy classification presently comprises the following modules:

Further information on the composition of the families and mechanistic details can be obtained via these pages and the corresponding Lexicon entries.

References

  1. ISBN:9780240521183 [StickWilliams2009]
  2. ISBN:9780854042562 [Sinnott2007]
  3. Laine RA. A calculation of all possible oligosaccharide isomers both branched and linear yields 1.05 x 10(12) structures for a reducing hexasaccharide: the Isomer Barrier to development of single-method saccharide sequencing or synthesis systems. Glycobiology. 1994 Dec;4(6):759-67. PubMed ID:7734838 | HubMed [Laine1994]
  4. ISBN:9780199569113 [TaylorDrickamer2011]
  5. Henrissat B, Claeyssens M, Tomme P, Lemesle L, and Mornon JP. Cellulase families revealed by hydrophobic cluster analysis. Gene. 1989 Sep 1;81(1):83-95. PubMed ID:2806912 | HubMed [Henrissat1989]
  6. Henrissat B. A classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem J. 1991 Dec 1;280 ( Pt 2):309-16. PubMed ID:1747104 | HubMed [Henrissat1991]
  7. Henrissat B and Bairoch A. New families in the classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem J. 1993 Aug 1;293 ( Pt 3):781-8. PubMed ID:8352747 | HubMed [Henrissat1993]
  8. Henrissat B and Bairoch A. Updating the sequence-based classification of glycosyl hydrolases. Biochem J. 1996 Jun 1;316 ( Pt 2):695-6. PubMed ID:8687420 | HubMed [Henrissat1996]
  9. Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. The Biochemist, vol. 30, no. 4., pp. 26-32. Download PDF version. [DaviesSinnott2008]
  10. Davies G and Henrissat B. Structures and mechanisms of glycosyl hydrolases. Structure. 1995 Sep 15;3(9):853-9. DOI:10.1016/S0969-2126(01)00220-9 | PubMed ID:8535779 | HubMed [DaviesHenrissat1995]
  11. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, and Henrissat B. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 2009 Jan;37(Database issue):D233-8. DOI:10.1093/nar/gkn663 | PubMed ID:18838391 | HubMed [Cantarel2009]
  12. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, and Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014 Jan;42(Database issue):D490-5. DOI:10.1093/nar/gkt1178 | PubMed ID:24270786 | HubMed [Lombard2013]
  13. Campbell JA, Davies GJ, Bulone V, and Henrissat B. A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities. Biochem J. 1997 Sep 15;326 ( Pt 3):929-39. PubMed ID:9334165 | HubMed [Campbell1997]
  14. Coutinho PM, Deleury E, Davies GJ, and Henrissat B. An evolving hierarchical family classification for glycosyltransferases. J Mol Biol. 2003 Apr 25;328(2):307-17. PubMed ID:12691742 | HubMed [Coutinho2003]
  15. ISBN:9780470016671 [Coutinho2009]
    Chapter 5: Coutinho PM, Rancurel C, Stam M, Bernard T, Couto FM, Danchin EGJ, Henrissat B. "Carbohydrate-active Enzymes Database: Principles and Classification of Glycosyltransferases."
  16. Lombard V, Bernard T, Rancurel C, Brumer H, Coutinho PM, and Henrissat B. A hierarchical classification of polysaccharide lyases for glycogenomics. Biochem J. 2010 Dec 15;432(3):437-44. DOI:10.1042/BJ20101185 | PubMed ID:20925655 | HubMed [Lombard2010]
  17. Garron ML and Cygler M. Structural and mechanistic classification of uronic acid-containing polysaccharide lyases. Glycobiology. 2010 Dec;20(12):1547-73. DOI:10.1093/glycob/cwq122 | PubMed ID:20805221 | HubMed [Garron2010]
  18. Levasseur A, Drula E, Lombard V, Coutinho PM, and Henrissat B. Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes. Biotechnol Biofuels. 2013 Mar 21;6(1):41. DOI:10.1186/1754-6834-6-41 | PubMed ID:23514094 | HubMed [Levasseur2013]
All Medline abstracts: PubMed | HubMed
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