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Difference between revisions of "Glycoside Hydrolase Families"
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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] | #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] | ||
#Lombard2013 pmid=24270786 | #Lombard2013 pmid=24270786 | ||
+ | #VocadloDavies2008 pmid=18558099 | ||
+ | #YipWithers2006 pmid=16495121 | ||
</biblio> | </biblio> | ||
</biblio> | </biblio> |
Revision as of 18:49, 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. 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.
- Transglycosidases: Sequence analysis classifies transglycosidases with retaining glycoside hydrolases. According to all available evidencetransglycosidases andglycoside hydrolases use the same mechanism, except that a sugar or some other group, rather than water, acts as the nucleophile.
- 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.
- 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.
- 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.
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
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.
- 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
- 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 9 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 directly, or via this form.
There are currently 41 Glycoside Hydrolase Family pages in CAZypedia that have not been assigned to a Responsible Curator.
- GH14
- GH24
- GH59
- GH71
- GH87
- GH90
- GH91
- GH96
- GH100
- GH108
- GH111
- GH118
- GH122
- GH132
- GH133
- GH148
- GH149
- GH150
- GH152
- GH153
- GH159
- GH154
- GH156
- GH157
- GH160
- GH161
- GH163
- GH165
- GH166
- GH167
- GH169
- GH175
- GH176
- GH177
- GH178
- GH180
- GH181
- GH182
- GH183
- GH184
- GH185
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 (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 |
- 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 |
- 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 |
- 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 |
- 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 |
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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
- 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 |
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