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Difference between revisions of "Carbohydrate-active enzymes"

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* [[Author]]s: ^^^Stephen Withers^^^, ^^^Spencer Williams^^^, and ^^^Harry Brumer^^^
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* [[Author]]s: [[User:Steve Withers|Stephen Withers]], [[User:Spencer Williams|Spencer Williams]], and [[User:Harry Brumer|Harry Brumer]]
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* [[Responsible Curator]]:  ^^^Spencer Williams^^^
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* [[Responsible Curator]]:  [[User:Spencer Williams|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 <cite>Laine1994</cite>. 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.
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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 <cite>StickWilliams2009 Sinnott2007</cite>. 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 <cite>Laine1994</cite>. Further, carbohydrates can be linked to other, non-carbohydrate molecules to generate a wide range of glycoconjugates <cite>TaylorDrickamer2011</cite>. Reflecting this structural diversity, there is a large diversity of enzymes involved in the biosynthesis, modification, binding and catabolism of carbohydrates.
  
 
==The <U>C</U>arbohydrate <U>A</U>ctive En<U>Zy</U>me ("CAZy") classification==
 
==The <U>C</U>arbohydrate <U>A</U>ctive En<U>Zy</U>me ("CAZy") classification==
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The <U>C</U>arbohydrate <U>A</U>ctive En<U>Zy</U>me (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^^^ (<cite>Henrissat1991 Henrissat1993 Henrissat1996</cite>; see <cite>DaviesSinnott2008</cite> 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 <cite>DaviesHenrissat1995</cite>.  Since its inception, the CAZy classification and associated database has undergone continually active curation, including the addition of new enzyme and associated module classes <cite>Cantarel2009 Lombard2013</cite>.  Hence, the CAZy classification presently comprises [[Glycoside Hydrolase Families]] <cite>Henrissat1991 Henrissat1993 Henrissat1996</cite>, [[Glycosyltransferase Families]] <cite>Campbell1997 Coutinho2003 Coutinho2009</cite>, [[Polysaccharide Lyase Families]] <cite>Lombard2010</cite>, [[Auxiliary Activity Families]] <cite>Levasseur2013</cite>, and [[Carbohydrate Binding Module Families]].  Further information on the composition of the families and mechanistic details can be obtained via these pages.
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The <U>C</U>arbohydrate <U>A</U>ctive En<U>Zy</U>me (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 [[User:Bernard Henrissat|Bernard Henrissat]] (<cite>Henrissat1989 Henrissat1991 Henrissat1993 Henrissat1996</cite>; see <cite>DaviesSinnott2008</cite> 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 <cite>DaviesHenrissat1995</cite>.  Since its inception, the CAZy classification and associated database has undergone continually active curation, including the addition of new enzyme and associated module classes <cite>Cantarel2009 Lombard2013 Drula2022</cite>.  Hence, the CAZy classification presently comprises the following modules:
 +
* [[Glycosyltransferase Families]] <cite>Campbell1997 Coutinho2003 Coutinho2009</cite>
 +
* [[Glycoside Hydrolase Families]] <cite>Henrissat1991 Henrissat1993 Henrissat1996</cite>
 +
* [[Polysaccharide Lyase Families]] <cite>Lombard2010 Garron2010</cite>
 +
* [[Carbohydrate Esterase Families]] <cite>Davies2005 Biely2012</cite>
 +
* [[Auxiliary Activity Families]] <cite>Levasseur2013</cite>
 +
* [[Carbohydrate Binding Module Families]] (non-catalytic; included due to their association with catalytic modules) <cite>Cantarel2009</cite>.   
  
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<!--
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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.
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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.
 
−
-->
 
  
 
== References ==
 
== References ==
 
<biblio>
 
<biblio>
 +
#StickWilliams2009 isbn=9780240521183
 
#Laine1994 pmid=7734838
 
#Laine1994 pmid=7734838
−
#DaviesSinnott2008 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). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]
+
#TaylorDrickamer2011 isbn=9780199569113
−
#Cantarel2009 pmid=18838391
 
−
#Lombard2013 pmid=24270786
 
−
#Lairson2008 pmid=18518825
 
−
#Lombard2010 pmid=20925655
 
−
#Garron2010 pmid=20805221
 
−
#Levasseur2013 pmid=23514094
 
−
#Boraston2004 pmid=15214846
 
−
#Shoseyov2006 pmid=16760304
 
−
#Hashimoto2006 pmid=17131061
 
−
#Guillen2010 pmid=19908036
 
−
#Gilbert2013 pmid=23769966
 
−
#VocadloDavies2008 pmid=18558099
 
−
#YipWithers2006 pmid=16495121
 
 
#Henrissat1991 pmid=1747104
 
#Henrissat1991 pmid=1747104
 
#Henrissat1993 pmid=8352747
 
#Henrissat1993 pmid=8352747
 
#Henrissat1996 pmid=8687420
 
#Henrissat1996 pmid=8687420
 
#DaviesHenrissat1995 pmid=8535779
 
#DaviesHenrissat1995 pmid=8535779
−
#Levasseur2013 pmid=23514094
+
#DaviesSinnott2008 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. [https://doi.org/10.1042/BIO03004026 DOI:10.1042/BIO03004026].
 +
#Cantarel2009 pmid=18838391
 +
#Lombard2013 pmid=24270786
 +
#Lombard2010 pmid=20925655
 
#Campbell1997 pmid=9334165
 
#Campbell1997 pmid=9334165
 
#Coutinho2003 pmid=12691742
 
#Coutinho2003 pmid=12691742
−
#Coutinho2009 isbn=9780470016671
+
#Coutinho2009 isbn=9780470016671 // ''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."
 +
#Garron2010 pmid=20805221
 +
#Levasseur2013 pmid=23514094
 +
#Henrissat1989 pmid=2806912
 +
#Sinnott2007 isbn=9780854042562
 +
#Davies2005 pmid=16263268
 +
#Biely2012 pmid=22580218
  
−
// ''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."
+
#Drula2022 pmid=34850161
 
</biblio>
 
</biblio>
  
 
[[Category:Definitions and explanations]]
 
[[Category:Definitions and explanations]]

Latest revision as of 11:28, 4 July 2023

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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, 13]. 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. Michael Sinnott. (2007) Carbohydrate Chemistry and Biochemistry. Royal Society of Chemistry. [Sinnott2007]
  3. 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]
  4. Maureen E. Taylor and Kurt Drickamer. (2011-04-21) Introduction to Glycobiology. Oxford University Press, USA. [TaylorDrickamer2011]
  5. Henrissat B, Claeyssens M, Tomme P, Lemesle L, and Mornon JP. (1989). Cellulase families revealed by hydrophobic cluster analysis. Gene. 1989;81(1):83-95. DOI:10.1016/0378-1119(89)90339-9 | PubMed ID:2806912 [Henrissat1989]
  6. 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]
  7. 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]
  8. 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]

  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. DOI:10.1042/BIO03004026.

    [DaviesSinnott2008]
  10. 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]
  11. 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]
  12. 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]
  13. Drula E, Garron ML, Dogan S, Lombard V, Henrissat B, and Terrapon N. (2022). The carbohydrate-active enzyme database: functions and literature. Nucleic Acids Res. 2022;50(D1):D571-D577. DOI:10.1093/nar/gkab1045 | PubMed ID:34850161 [Drula2022]
  14. 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]
  15. 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]
  16. 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."

  17. 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]
  18. 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]
  19. Davies GJ, Gloster TM, and Henrissat B. (2005). Recent structural insights into the expanding world of carbohydrate-active enzymes. Curr Opin Struct Biol. 2005;15(6):637-45. DOI:10.1016/j.sbi.2005.10.008 | PubMed ID:16263268 [Davies2005]
  20. Biely P (2012). Microbial carbohydrate esterases deacetylating plant polysaccharides. Biotechnol Adv. 2012;30(6):1575-88. DOI:10.1016/j.biotechadv.2012.04.010 | PubMed ID:22580218 [Biely2012]
  21. 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]

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