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Difference between revisions of "Carbohydrate-active enzymes"

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{{CuratorApproved}}
 
{{CuratorApproved}}
* [[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]]
* [[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 <cite>StickWilliams2009</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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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==
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 the following modules:
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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>
 
* [[Glycoside Hydrolase Families]] <cite>Henrissat1991 Henrissat1993 Henrissat1996</cite>
* [[Glycosyltransferase Families]] <cite>Campbell1997 Coutinho2003 Coutinho2009</cite>
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* [[Polysaccharide Lyase Families]] <cite>Lombard2010 Garron2010</cite>
* [[Polysaccharide Lyase Families]] <cite>Lombard2010</cite>
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* [[Carbohydrate Esterase Families]] <cite>Davies2005 Biely2012</cite>
 
* [[Auxiliary Activity Families]] <cite>Levasseur2013</cite>
 
* [[Auxiliary Activity Families]] <cite>Levasseur2013</cite>
* [[Carbohydrate Binding Module Families]].   
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* [[Carbohydrate Binding Module Families]] (non-catalytic; included due to their association with catalytic modules) <cite>Cantarel2009</cite>.   
  
 
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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== References ==
 
== References ==
 
<biblio>
 
<biblio>
#TaylorDrickamer2011 isbn=9780199569113
 
 
#StickWilliams2009 isbn=9780240521183
 
#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
 +
#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 // ''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."
 
#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
 +
 +
#Drula2022 pmid=34850161
 
</biblio>
 
</biblio>
  
 
[[Category:Definitions and explanations]]
 
[[Category:Definitions and explanations]]

Latest revision as of 12:28, 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

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Error fetching PMID 1747104:
Error fetching PMID 8352747:
Error fetching PMID 8687420:
Error fetching PMID 8535779:
Error fetching PMID 18838391:
Error fetching PMID 24270786:
Error fetching PMID 20925655:
Error fetching PMID 9334165:
Error fetching PMID 12691742:
Error fetching PMID 20805221:
Error fetching PMID 23514094:
Error fetching PMID 2806912:
Error fetching PMID 16263268:
Error fetching PMID 22580218:
Error fetching PMID 34850161:
  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. Error fetching PMID 7734838: [Laine1994]
  4. Maureen E. Taylor and Kurt Drickamer. (2011-04-21) Introduction to Glycobiology. Oxford University Press, USA. [TaylorDrickamer2011]
  5. Error fetching PMID 2806912: [Henrissat1989]
  6. Error fetching PMID 1747104: [Henrissat1991]
  7. Error fetching PMID 8352747: [Henrissat1993]
  8. Error fetching PMID 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. Error fetching PMID 8535779: [DaviesHenrissat1995]
  11. Error fetching PMID 18838391: [Cantarel2009]
  12. Error fetching PMID 24270786: [Lombard2013]
  13. Error fetching PMID 34850161: [Drula2022]
  14. Error fetching PMID 9334165: [Campbell1997]
  15. Error fetching PMID 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. Error fetching PMID 20925655: [Lombard2010]
  18. Error fetching PMID 20805221: [Garron2010]
  19. Error fetching PMID 16263268: [Davies2005]
  20. Error fetching PMID 22580218: [Biely2012]
  21. Error fetching PMID 23514094: [Levasseur2013]

All Medline abstracts: PubMed