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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]]).
 
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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The [[Lexicon]] entry [[Glycoside hydrolases]] contains an introduction and overview to this class of enzymes. The classification mirrors that of the [http://www.cazy.org CAZy database] <cite>#DaviesSinnott2008 Cantarel2009 Lombard2013</cite>, which itself is based on the sequence-based families of glycoside hydrolases as described in <cite>Henrissat1991 Henrissat1993 Henrissat1996 Davies1995 Henrissat1997</cite>.
 
 
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==Background==
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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 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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== Curator Approved ==
 
== Curator Approved ==

Revision as of 18:38, 11 December 2013

This pages 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 or unassigned (i.e. lacking a Responsible Curator and Author).

Background

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.

  • Phosphorylases: Sequence similarly classifies many, but 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.

Seminal publications on GH classification: [1, 2, 3].

Key reviews on GH and related mechanisms (e.g. GH4 enzymes and GH31 lyases): [4, 5].


Curator Approved

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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

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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

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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 directly, or via this form.

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. 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]
  5. 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]
  6. 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]

  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. 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]

All Medline abstracts: PubMed

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