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Difference between revisions of "Carbohydrate-active enzymes"

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Further information on the composition of the families and mechanistic details can be obtained via these pages and the corresponding [[Lexicon]] entries.
 
Further information on the composition of the families and mechanistic details can be obtained via these pages and the corresponding [[Lexicon]] entries.
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===Glycoside hydrolases (GH)===
 
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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.
 
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* [[Transglycosidases]]: Sequence analysis classifies [[transglycosidases]] with [[retaining]] [[glycoside hydrolases]]. 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.
 
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* [[Phosphorylases]]: Sequence similarly classifies many, but not 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 synthesis of glycosidic linkages form sugar-1-phosphates. Again, GH-like [[phosphorylases]] share mechanistic similarities with [[glycoside hydrolases]].
 
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* [[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]].
 
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* [[NAD-dependent hydrolysis|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]].
 
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''Seminal publications on GH classification: <cite>Henrissat1991 Henrissat1993 Henrissat1996</cite>.''
 
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''Key reviews on GH and related mechanisms (''e.g.'' GH4 enzymes and GH31 lyases): <cite>VocadloDavies2008 YipWithers2006</cite>.''
 
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===Polysaccharide lyases (PL)===
 
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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.
 
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''Formal introduction of the PL classification:  <cite>Lombard2010</cite>.''
 
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''Reviews of PL mechanisms: <cite>YipWithers2006 Lombard2010 Garron2010</cite>.''
 
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===Auxiliary activities (AA)===
 
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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
 
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new category, the "Auxiliary Activities" <cite>Levasseur2013</cite>. 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.
 
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''Introduction of the AA classification: <cite>Levasseur2013</cite>.''
 
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===Glycosyltransferases (GT)===
 
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The principal enzymes that catalyze glycoside synthesis are [[glycosyltransferases]]. Glycosyltransferases utilize various sugar-1-phosphate derivatives including:
 
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* Sugar mono- or diphosphonucleotides, in which case the resulting enzymes are referred to as Leloir glycosyltransferases.
 
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* Non-nucleotide carbohydrate donors including various sugar polyprenol mono- or diphosphates, in which case the enzymes are referred to as non-Leloir glycosyltransferases.
 
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* Sugar-1-phosphates and -pyrophosphates, in which case the enzymes are referred to as phosphorylases or pyrophosphorylases. Only some of such enzymes are classified as GTs on the basis of sequence (''e.g.'' glycogen phosphorylase of [[GT35]]), others are classified as GHs.
 
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''Seminal publications on GT classification: <cite>Campbell1997 Coutinho2003 Coutinho2009</cite>.''
 
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''Key GT review: <cite>Lairson2008</cite>.''
 
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===Carbohydrate binding modules (CBM)===
 
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For a comprehensive discussion of CBMs see the [[Carbohydrate-binding modules]] Lexicon page.
 
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== References ==
 
== References ==

Revision as of 20:09, 17 December 2013

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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]. 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 [2]. Further, carbohydrates can be linked to other, non-carbohydrate molecules to generate a wide range of glycoconjugates [3]. 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 are active on carbohydrate structures, which originated with the seminal classification of glycoside hydrolases by ^^^Bernard Henrissat^^^ ([4, 5, 6]; see [7] 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 [8]. Since its inception, the CAZy classification and associated database has undergone continually active curation, including the addition of new enzyme and associated module classes [9, 10]. 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. [StickWilliams2009]
  2. Laine RA (1994). 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;4(6):759-67. DOI:10.1093/glycob/4.6.759 | PubMed ID:7734838 [Laine1994]
  3. Maureen E. Taylor and Kurt Drickamer. (2011-04-21) Introduction to Glycobiology. Oxford University Press, USA. [TaylorDrickamer2011]
  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 | PubMed ID:1747104 [Henrissat1991]
  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 | PubMed ID:8352747 [Henrissat1993]
  6. 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 | PubMed ID:8687420 [Henrissat1996]

  7. 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

    [DaviesSinnott2008]
  8. 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 | PubMed ID:8535779 [DaviesHenrissat1995]
  9. 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 | PubMed ID:18838391 [Cantarel2009]
  10. 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 | PubMed ID:24270786 [Lombard2013]
  11. 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 | PubMed ID:9334165 [Campbell1997]
  12. 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 | PubMed ID:12691742 [Coutinho2003]
  13. Claus-Wilhelm von der Lieth, Thomas Luetteke, and Martin Frank. (2010-01-19) Bioinformatics for Glycobiology and Glycomics: An Introduction. Wiley. [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."

  14. 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 | PubMed ID:20925655 [Lombard2010]
  15. 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 | PubMed ID:23514094 [Levasseur2013]
  16. 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 | PubMed ID:18518825 [Lairson2008]
  17. 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 | PubMed ID:20805221 [Garron2010]
  18. 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 | PubMed ID:15214846 [Boraston2004]
  19. 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 | PubMed ID:16760304 [Shoseyov2006]
  20. 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 | PubMed ID:17131061 [Hashimoto2006]
  21. 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 | PubMed ID:19908036 [Guillen2010]
  22. 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 | PubMed ID:23769966 [Gilbert2013]
  23. 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 | PubMed ID:18558099 [VocadloDavies2008]
  24. 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 | PubMed ID:16495121 [YipWithers2006]

All Medline abstracts: PubMed

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