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Difference between revisions of "Carbohydrate-active enzymes"

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* [[Author]]: [[User:StephenWithers|Stephen Withers]]
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* [[Responsible Curator]]:  [[User:SpencerWilliams|Spencer Williams]]
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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]]:  [[User:Spencer Williams|Spencer Williams]]
 
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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''.
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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.
  
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==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 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</cite>.  Hence, the CAZy classification presently comprises the following modules:
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* [[Glycosyltransferase Families]] <cite>Campbell1997 Coutinho2003 Coutinho2009</cite>
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* [[Glycoside Hydrolase Families]] <cite>Henrissat1991 Henrissat1993 Henrissat1996</cite>
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* [[Polysaccharide Lyase Families]] <cite>Lombard2010 Garron2010</cite>
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* [[Carbohydrate Esterase Families]] <cite>Davies2005 Biely2012</cite>
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* [[Auxiliary Activity Families]] <cite>Levasseur2013</cite>
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* [[Carbohydrate Binding Module Families]] (non-catalytic; included due to their association with catalytic modules) <cite>Cantarel2009</cite>. 
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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.
  
 
== References ==
 
== References ==
 
<biblio>
 
<biblio>
#1 pmid=17323919
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#StickWilliams2009 isbn=9780240521183
 
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#Laine1994 pmid=7734838
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#TaylorDrickamer2011 isbn=9780199569113
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#Henrissat1991 pmid=1747104
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#Henrissat1993 pmid=8352747
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#Henrissat1996 pmid=8687420
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#DaviesHenrissat1995 pmid=8535779
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#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 Download PDF version].
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#Cantarel2009 pmid=18838391
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#Lombard2013 pmid=24270786
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#Lombard2010 pmid=20925655
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#Campbell1997 pmid=9334165
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#Coutinho2003 pmid=12691742
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#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."
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#Garron2010 pmid=20805221
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#Levasseur2013 pmid=23514094
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#Henrissat1989 pmid=2806912
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#Sinnott2007 isbn=9780854042562
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#Davies2005 pmid=16263268
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#Biely2012 pmid=22580218
 
</biblio>
 
</biblio>
  
<!-- Please delete the "<nowiki>" and "</nowiki> tags before saving.) -->
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[[Category:Definitions and explanations]]
<nowiki>[[Category:Glycoside Hydrolase Families]]</nowiki>
 

Latest revision as of 14:10, 20 December 2021

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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. Robert V. Stick and Spencer J. Williams. (2009) Carbohydrates. Elsevier Science. [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. [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. Download PDF version.

    [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. 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]
  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 | PubMed ID:12691742 [Coutinho2003]
  15. 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."

  16. 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]
  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. 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]
  19. 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]
  20. 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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