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Difference between revisions of "Glycoside Hydrolase Families"

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This pages lists all the Glycoside Hydrolase (GH) Family pages in ''CAZypedia'' that have been given [[:Category:Curator approved|Curator Approved]] status, as well as those that are currently [[:Category:Under construction|under construction]] or [[:Category:Unassigned pages|unassigned]] (''i.e.'' lacking a [[Responsible Curator]] and [[Author]]).
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''This page lists all the Glycoside Hydrolase (GH) Family pages in ''CAZypedia'' that have been given [[:Category:Curator approved|Curator Approved]] status, as well as those that are currently [[:Category:Under construction|under construction]], [[:Category:Unassigned pages|unassigned]] (''i.e.'' lacking a [[Responsible Curator]] and [[Author]]), or deleted.''
  
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__TOC__
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== Overview ==
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==Background==
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The term [[glycoside hydrolase|glycoside hydrolase (GH)]] (''alternatively, [[glycoside hydrolase|glycosidase]]'') formally refers to enzymes that catalyze the hydrolytic cleavage of the glycosidic bond to give the carbohydrate hemiacetal. Detailed explanations of the distinct catalytic mechanisms employed by these enzymes can be found on the [[glycoside hydrolase]] lexicon page.  Since the seminal [[sequence-based classification]] of GHs into families, it has subsequently been observed that some of these families also group non-hydrolytic enzymes and proteins, due to sequence and structural similarity <cite>Henrissat1991 Henrissat1993 Henrissat1996 Henrissat1997 DaviesSinnott2008 Davies1995 VocadloDavies2008 YipWithers2006</cite>.  In many cases, these alternative activities bear some degree of mechanistic similarity (''e.g.'', conserved catalytic residues or enzyme intermediates) to the eponymous enzymes:
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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. Additionally, 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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* [[Transglycosylases]] are mechanistically related to [[retaining]] [[glycoside hydrolases]], with the exception that a sugar (or another nucleophile), rather than water, acts as the acceptor substrate to yield glycosidic bond exchange.
  
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* [[Phosphorylases]]: Sequence similarly classifies many, but not all (see [[glycosyltransferases]] for exceptions) [[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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* [[Phosphorylases]] cleave glycosidic bonds using phosphate as a nucleophile to yield sugar-1-phosphates; this reaction is readily reversible, allowing the synthesis of glycosidic linkages.  Sequence classifies many, but not all (see [[glycosyltransferases]] for exceptions) [[phosphorylases]] with [[retaining]] or [[inverting]] [[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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* [[Alpha-glucan lyases]] are found within family [[GH31]] and degrade &alpha;-(1-4)-linked glucans (''e.g.'' starch) and oligosaccharides via an elimination mechanism that yields an enol (unsaturated) product that tautomerises to its keto form, 1,5-anhydro fructose.
  
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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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* [[NAD-dependent hydrolysis|NAD-dependent glycoside hydrolases]] of families [[GH4]] and [[GH109]] use nicotinamide adenine dinucleotide as redox cofactor to activate the sugar ring for glycosidic bond cleavage by elimination.
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''Seminal publications on GH classification: <cite>Henrissat1991 Henrissat1993 Henrissat1996 Henrissat1997 DaviesSinnott2008</cite>.''
 
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''Key reviews on GH and related mechanisms (''e.g.'' GH4 enzymes and GH31 lyases): <cite>Davies1995 VocadloDavies2008 YipWithers2006</cite>.''
 
  
 
== Curator Approved ==
 
== Curator Approved ==
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== Unassigned pages ==
 
== Unassigned pages ==
 
<blockquote class="toccolours" style="float:none; padding: 10px 15px 10px 15px; display:table;">
 
<blockquote class="toccolours" style="float:none; padding: 10px 15px 10px 15px; display:table;">
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[[File:Blank user-200px.png|left|40px]]The following [[:Category:Unassigned pages|Unassigned pages]] are currently lacking a [[Responsible Curator]] and one or more [[Author]]s. If you are an expert on any of these families and would like to help us improve ''CAZypedia'' by getting involved with the production and maintenance of the corresponding page(s), please contact a member of the [[Board of Curators]] directly, or via [[Special:Contact|this form]].
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[[File:Blank user-200px.png|left|40px]]The following [[:Category:Unassigned pages|Unassigned pages]] are currently lacking a [[Responsible Curator]] and one or more [[Author]]s. If you are an expert on any of these families and would like to help us improve ''CAZypedia'' by getting involved with the production and maintenance of the corresponding page(s), please contact a member of the [[Board of Curators]].
 
</blockquote>
 
</blockquote>
 
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{{#dpl:
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== References ==
 
== References ==
 
<biblio>
 
<biblio>
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#Cantarel2009 pmid=18838391
 
 
#Henrissat1991 pmid=1747104
 
#Henrissat1991 pmid=1747104
 
#Henrissat1993 pmid=8352747
 
#Henrissat1993 pmid=8352747
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#Davies1995 pmid=8535779
 
#Davies1995 pmid=8535779
 
#Henrissat1997 pmid=9345621
 
#Henrissat1997 pmid=9345621
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#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]
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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. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
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#Lombard2013 pmid=24270786
 
 
#VocadloDavies2008 pmid=18558099
 
#VocadloDavies2008 pmid=18558099
 
#YipWithers2006 pmid=16495121
 
#YipWithers2006 pmid=16495121
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</biblio>
 
 
</biblio>
 
</biblio>

Revision as of 08:53, 21 August 2018

This page lists all the Glycoside Hydrolase (GH) Family pages in CAZypedia that have been given Curator Approved status, as well as those that are currently under construction, unassigned (i.e. lacking a Responsible Curator and Author), or deleted.

Overview

The term glycoside hydrolase (GH) (alternatively, glycosidase) formally refers to enzymes that catalyze the hydrolytic cleavage of the glycosidic bond to give the carbohydrate hemiacetal. Detailed explanations of the distinct catalytic mechanisms employed by these enzymes can be found on the glycoside hydrolase lexicon page. Since the seminal sequence-based classification of GHs into families, it has subsequently been observed that some of these families also group non-hydrolytic enzymes and proteins, due to sequence and structural similarity [1, 2, 3, 4, 5, 6, 7, 8]. In many cases, these alternative activities bear some degree of mechanistic similarity (e.g., conserved catalytic residues or enzyme intermediates) to the eponymous enzymes:

  • Alpha-glucan lyases are found within family GH31 and degrade α-(1-4)-linked glucans (e.g. starch) and oligosaccharides via an elimination mechanism that yields an enol (unsaturated) product that tautomerises to its keto form, 1,5-anhydro fructose.

Curator Approved

Approve icon-50px.png

These pages have been approved by the Responsible Curator as essentially complete. CAZypedia is a living document, so further improvement of these pages is still possible; please see the individual pages for more information.

There are currently 139 Curator approved Glycoside Hydrolase (GH) Family pages in CAZypedia.

Under construction

Under construction icon-blue-48px.png

These pages are currently under construction in CAZypedia. As such, the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information on these pages should therefore be considered to be under revision and may be subject to major changes.

There are currently 9 Glycoside Hydrolase Family pages under construction in CAZypedia.

Unassigned pages

Blank user-200px.png

The following Unassigned pages are currently lacking a Responsible Curator and one or more Authors. If you are an expert on any of these families and would like to help us improve CAZypedia by getting involved with the production and maintenance of the corresponding page(s), please contact a member of the Board of Curators.

There are currently 41 Glycoside Hydrolase Family pages in CAZypedia that have not been assigned to a Responsible Curator.

Deleted families

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The following families have been deleted from the CAZy database. Please see the individual CAZypedia pages and links to the corresponding CAZy DB pages for specific explanations.

There are currently 8 pages in CAZypedia that describe Glycoside Hydrolase families deleted from the CAZy DB.

References

  1. 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]
  2. 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]
  3. 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]
  4. Henrissat B and Davies G. (1997). Structural and sequence-based classification of glycoside hydrolases. Curr Opin Struct Biol. 1997;7(5):637-44. DOI:10.1016/s0959-440x(97)80072-3 | PubMed ID:9345621 [Henrissat1997]

  5. 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]
  6. 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 [Davies1995]
  7. 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]
  8. 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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