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Difference between revisions of "Glycoside Hydrolase Families"
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== Overview == | == Overview == | ||
| − | 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 < | + | 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>Henrissat1989 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: |
* [[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. | * [[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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* [[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. | * [[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. | ||
| − | * [[NAD-dependent hydrolysis|NAD-dependent glycoside hydrolases]] of families [[GH4]] and [[ | + | * [[NAD-dependent hydrolysis|NAD-dependent glycoside hydrolases]] of families [[GH4]], [[GH109]], [[GH177]], [[GH179]] and [[GH188]] use nicotinamide adenine dinucleotide as redox cofactor to activate the sugar ring for glycosidic bond cleavage by elimination. |
== Curator Approved == | == Curator Approved == | ||
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|category=Glycoside Hydrolase Families | |category=Glycoside Hydrolase Families | ||
|category=Under construction | |category=Under construction | ||
| + | |mode=userformat | ||
|resultsheader=\nThere are currently %PAGES% Glycoside Hydrolase Family pages [[:Category:Under construction|under construction]] in ''CAZypedia''.\n | |resultsheader=\nThere are currently %PAGES% Glycoside Hydrolase Family pages [[:Category:Under construction|under construction]] in ''CAZypedia''.\n | ||
|noresultsheader=\nThere are currently no pages in this category.\n | |noresultsheader=\nThere are currently no pages in this category.\n | ||
| + | |allowcachedresults=no | ||
| + | }} | ||
| + | <div style="-webkit-column-count:10;column-count:10;"> | ||
| + | {{#dpl: | ||
| + | |category=Glycoside Hydrolase Families | ||
| + | |category=Under construction | ||
|ordermethod=sortkey | |ordermethod=sortkey | ||
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|allowcachedresults=no | |allowcachedresults=no | ||
}} | }} | ||
| − | + | </div> | |
== 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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|category=Glycoside Hydrolase Families | |category=Glycoside Hydrolase Families | ||
|category=Unassigned pages | |category=Unassigned pages | ||
| + | |mode=userformat | ||
|resultsheader=\nThere are currently %PAGES% Glycoside Hydrolase Family pages in ''CAZypedia'' that have not been assigned to a [[Responsible Curator]].\n | |resultsheader=\nThere are currently %PAGES% Glycoside Hydrolase Family pages in ''CAZypedia'' that have not been assigned to a [[Responsible Curator]].\n | ||
|noresultsheader=\nThere are currently no pages in this category.\n | |noresultsheader=\nThere are currently no pages in this category.\n | ||
| + | |allowcachedresults=no | ||
| + | }} | ||
| + | <div style="-webkit-column-count:10;column-count:10;"> | ||
| + | {{#dpl: | ||
| + | |category=Glycoside Hydrolase Families | ||
| + | |category=Unassigned pages | ||
|ordermethod=sortkey | |ordermethod=sortkey | ||
|order=ascending | |order=ascending | ||
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|allowcachedresults=no | |allowcachedresults=no | ||
}} | }} | ||
| − | + | </div> | |
== Deleted families == | == Deleted families == | ||
<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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|category=Glycoside Hydrolase Families | |category=Glycoside Hydrolase Families | ||
|category=Deleted families | |category=Deleted families | ||
| + | |mode=userformat | ||
|resultsheader=\nThere are currently %PAGES% pages in ''CAZypedia'' that describe Glycoside Hydrolase families deleted from the CAZy DB.\n | |resultsheader=\nThere are currently %PAGES% pages in ''CAZypedia'' that describe Glycoside Hydrolase families deleted from the CAZy DB.\n | ||
|noresultsheader=\nThere are currently no pages in this category.\n | |noresultsheader=\nThere are currently no pages in this category.\n | ||
| + | |allowcachedresults=no | ||
| + | }} | ||
| + | <div style="-webkit-column-count:10;column-count:10;">{{#dpl: | ||
| + | |category=Glycoside Hydrolase Families | ||
| + | |category=Deleted families | ||
|ordermethod=sortkey | |ordermethod=sortkey | ||
|order=ascending | |order=ascending | ||
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}} | }} | ||
| + | </div> | ||
== References == | == References == | ||
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#Davies1995 pmid=8535779 | #Davies1995 pmid=8535779 | ||
#Henrissat1997 pmid=9345621 | #Henrissat1997 pmid=9345621 | ||
| − | #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 | + | #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]. |
#VocadloDavies2008 pmid=18558099 | #VocadloDavies2008 pmid=18558099 | ||
#YipWithers2006 pmid=16495121 | #YipWithers2006 pmid=16495121 | ||
</biblio> | </biblio> | ||
Latest revision as of 13:23, 17 December 2023
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, 9]. In many cases, these alternative activities bear some degree of mechanistic similarity (e.g., conserved catalytic residues or enzyme intermediates) to the eponymous enzymes:
- 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.
- 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.
- 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.
- NAD-dependent glycoside hydrolases of families GH4, GH109, GH177, GH179 and GH188 use nicotinamide adenine dinucleotide as redox cofactor to activate the sugar ring for glycosidic bond cleavage by elimination.
Curator Approved
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 140 Curator approved Glycoside Hydrolase (GH) Family pages in CAZypedia.
- GH1
- GH2
- GH3
- GH4
- GH5
- GH6
- GH7
- GH8
- GH9
- GH10
- GH11
- GH12
- GH13
- GH15
- GH16
- GH17
- GH18
- GH19
- GH20
- GH21
- GH22
- GH23
- GH25
- GH26
- GH27
- GH28
- GH29
- GH30
- GH31
- GH32
- GH33
- GH34
- GH35
- GH36
- GH37
- GH38
- GH39
- GH40
- GH41
- GH42
- GH43
- GH44
- GH45
- GH46
- GH47
- GH48
- GH49
- GH50
- GH51
- GH52
- GH53
- GH54
- GH55
- GH57
- GH58
- GH60
- GH61
- GH62
- GH63
- GH64
- GH65
- GH66
- GH67
- GH68
- GH69
- GH70
- GH72
- GH73
- GH74
- GH75
- GH76
- GH77
- GH78
- GH79
- GH80
- GH81
- GH82
- GH84
- GH85
- GH86
- GH88
- GH89
- GH92
- GH93
- GH94
- GH95
- GH97
- GH98
- GH99
- GH101
- GH102
- GH103
- GH104
- GH105
- GH106
- GH107
- GH109
- GH110
- GH112
- GH113
- GH114
- GH115
- GH116
- GH117
- GH119
- GH120
- GH121
- GH123
- GH124
- GH125
- GH127
- GH128
- GH129
- GH130
- GH131
- GH134
- GH135
- GH136
- GH137
- GH138
- GH139
- GH140
- GH141
- GH144
- GH145
- GH146
- GH147
- GH151
- GH155
- GH158
- GH162
- GH164
- GH168
- GH172
- GH173
- GH174
- GH186
- GH187
- GH188
- GH189
Under construction
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 8 Glycoside Hydrolase Family pages under construction in CAZypedia.
Unassigned pages
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. Undergraduate students, (post)graduate students, post-doctoral researchers, research associates, and professors are all welcomed to contribute!
There are currently 41 Glycoside Hydrolase Family pages in CAZypedia that have not been assigned to a Responsible Curator.
Deleted families
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
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
-
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.
- 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 |
- 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 |
- 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 |