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Glycoside Hydrolase family classification

Introduction

Glycoside hydrolases (EC 3.2.1.-) are a widespread group of enzymes which hydrolyse the glycosidic bond between two or more carbohydrates or between a carbohydrate and a non-carbohydrate moiety. The IUBMB Enzyme nomenclature of glycoside hydrolases is based on their substrate specificity and occasionally on their molecular mechanism; such a classification does not reflect (and was not intended to) the structural features of these enzymes. A classification of glycoside hydrolases in families based on amino acid sequence similarities has been proposed a few years ago. Because there is a direct relationship between sequence and folding similarities, such a classification:

(i) reflects the structural features of these enzymes better than their sole substrate specificity,

(ii) helps to reveal the evolutionary relationships between these enzymes,

(iii) provides a convenient tool to derive mechanistic information [1] [2]

(iv) illustrates the difficulty of deriving relationships between family membership and substrate specificity

The Carbohydrate-Active Enzymes database (CAZy) provides a continuously updated list of the glycoside hydrolase families. Because the fold of proteins is better conserved than their sequences, some of the families can be grouped in ’clans’ :
(i) when new sequences are found to be related to more than one family,
(ii) when the sensitivity of sequence comparison methods is increased or
(iii) when structural determinations demonstrate the resemblance between members of different families [3]

The established ’clans’ are given in form of a table below.

Catalytic Mechanism

In most cases, the hydrolysis of the glycosidic bond is catalyzed by two amino acid residues of the enzyme: a general acid (proton donor) and a nucleophile/base [4]. Depending on the spatial position of these catalytic residues, hydrolysis occurs via overall retention or overall inversion of the anomeric configuration. For each family listed in the CAZy database, we indicate (when it is known) the stereochemical outcome of the reaction catalyzed as well as the type of amino-acid residues acting as a nucleophile/base and as a proton donor. In some cases, the catalytic nucleophile is not borne by the enzyme, and is replaced by the acetamido group at C-2 of the substrate [5]. A completely unrelated mechanism has been demonstrated recently for two families of glycosidases utilizing NAD+ as a cofactor [6] [7].

For a detailed description of the catalytic mechanism (and variations thereof) of glycoside hydrolases, please visit CAZypedia.

Tables for Direct Access

- GH Family Number

12345678910111213141516171819202122232425262728293031323334353637383940
41424344454647484950515253545556575859606162636465666768697071727374757677787980
81828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120
121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160
161162163164165166167168169170171172173174175176177178179180181182183
Non-Classified Sequences

- GH SubFamily Number

GH51245789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657
GH1312345678910111213141516171819202122232425262728293031323334353637383940414243444546
GH16123456789101112131415161718192021222324252627
GH1912
GH3012345678910
GH311234567891011121314151617181920
GH431234567891011121314151617181920212223242526272829303132333435363739
GH451234
GH511234567891011121314
GH55123
GH6812
GH13012345678910111213141516

- GH Classification Statistics

Modules in present families 1320845
Non-Classified modules 33092

- GH Clans of Related Families

GH-A(β/α)81 2 5 10 17 26 30 35 39 42 50 51 53 59 72 79 86 113 128 140 147 148 157 158 164 167 169 173
GH-Bβ-jelly roll7 16
GH-Cβ-jelly roll11 12
GH-D(β/α)827 31 36
GH-E6-fold β-propeller33 34 83 93
GH-F5-fold β-propeller43 62 117
GH-G(α/α)637 63 100
GH-H(β/α)813 70 77
GH-Iα+β24 80
GH-J5-fold β-propeller32 68
GH-K(β/α)818 20 85
GH-L(α/α)615 65 125 178
GH-M(α/α)68 48
GH-Nβ-helix28 49
GH-O(α/α)652 116
GH-P(α/α)6127 146
GH-Q(α/α)694 149 161
GH-R(β/α)829 107

- EC Activities found in GH families

2.4.1.- 1 3 13 16 17 27 32 33 35 70 72 94 130
2.4.1.2 15
2.4.1.4 13
2.4.1.5 70
2.4.1.7 13
2.4.1.8 65
2.4.1.9 68
2.4.1.10 32 68
2.4.1.18 13 57
2.4.1.19 13
2.4.1.20 94
2.4.1.24 31
2.4.1.25 13 57 77
2.4.1.30 149
2.4.1.31 94
2.4.1.49 94
2.4.1.64 65
2.4.1.67 36
2.4.1.82 36
2.4.1.97 149 161
2.4.1.99 32
2.4.1.100 32
2.4.1.140 70
2.4.1.161 31
2.4.1.207 16
2.4.1.211 112
2.4.1.216 65
2.4.1.230 65
2.4.1.243 32
2.4.1.247 112
2.4.1.248 66
2.4.1.279 65
2.4.1.280 94
2.4.1.281 130
2.4.1.319 130
2.4.1.320 130
2.4.1.321 94
2.4.1.329 13
2.4.1.332 65
2.4.1.333 94
2.4.1.339 130
2.4.1.340 130
2.4.1.359 13
2.4.1.387 31
2.4.99.16 13
3.1.1.72 11
3.1.1.73 10 62
3.2.1.- 1 2 3 5 10 13 16 18 20 27 28 29 30 32 33 35 36 38 42 43 45 49 56 62 73 79 88 90 91 92 93 95 105 110 111 113 115 127 129 135 136 139 140 153 160 163 166 167 169 172 178 183 NC
3.2.1.1 13 57 126
3.2.1.2 13 14
3.2.1.3 15 97
3.2.1.4 5 6 7 8 9 10 12 26 44 45 48 51 124 148
3.2.1.6 3 5 8 9 16 51
3.2.1.7 32
3.2.1.8 5 6 8 10 11 26 30 43 98
3.2.1.10 13 31
3.2.1.11 31 49 66
3.2.1.14 18 19 23
3.2.1.15 28
3.2.1.17 19 22 23 24 25 108 NC
3.2.1.18 33 34 83 156 177 181
3.2.1.20 4 13 31 76 97 122
3.2.1.21 1 2 3 5 16 30 39 116 131 175 180
3.2.1.22 4 27 31 36 57 97 110
3.2.1.23 1 2 5 16 35 42 50 54 147 165 173
3.2.1.24 38 92
3.2.1.25 1 2 5 113 164
3.2.1.26 32 68 100
3.2.1.28 13 15 37 65
3.2.1.31 1 2 3 79 137
3.2.1.32 8 26
3.2.1.33 13 133
3.2.1.35 16 56 84
3.2.1.36 79
3.2.1.37 1 2 3 5 8 10 30 39 43 51 52 54 120
3.2.1.38 1 3 30 35
3.2.1.39 5 16 17 55 64 81 128 152 157 158
3.2.1.40 33 78 106
3.2.1.41 13 57
3.2.1.45 1 3 5 116
3.2.1.46 5 59
3.2.1.48 13 31
3.2.1.49 27 36 109 129
3.2.1.50 89
3.2.1.51 29 95 151
3.2.1.52 2 3 18 20 84 179
3.2.1.53 123
3.2.1.54 13
3.2.1.55 2 3 10 43 51 54 62 159
3.2.1.57 49
3.2.1.58 3 5 16 55 128 132
3.2.1.59 71 87
3.2.1.63 95
3.2.1.64 32
3.2.1.65 32
3.2.1.67 4 28
3.2.1.68 13 176
3.2.1.70 13 15
3.2.1.71 144 162
3.2.1.72 43
3.2.1.73 5 8 9 11 12 16 17 26 148 NC
3.2.1.74 1 3 5 9 39
3.2.1.75 5 30
3.2.1.76 39
3.2.1.78 5 26 44 113 134
3.2.1.81 16 50 86 118
3.2.1.82 28
3.2.1.83 16
3.2.1.84 31 63
3.2.1.85 1
3.2.1.86 1 4
3.2.1.88 27 36 97
3.2.1.89 53 147
3.2.1.91 5 6 9 48
3.2.1.92 171
3.2.1.93 13
3.2.1.94 27
3.2.1.95 49
3.2.1.96 18 20 73 85
3.2.1.97 101
3.2.1.98 13
3.2.1.99 43
3.2.1.100 5 26
3.2.1.101 76
3.2.1.102 98
3.2.1.105 1
3.2.1.106 63
3.2.1.107 65
3.2.1.108 1 2
3.2.1.109 114
3.2.1.111 29
3.2.1.113 38 47 92
3.2.1.114 38
3.2.1.116 13
3.2.1.117 1
3.2.1.118 1
3.2.1.119 1
3.2.1.122 4
3.2.1.123 5
3.2.1.124 33
3.2.1.126 3
3.2.1.127 29
3.2.1.128 79
3.2.1.129 58
3.2.1.130 99
3.2.1.131 67 115
3.2.1.132 3 5 8 46 75 80
3.2.1.133 13 57
3.2.1.135 13
3.2.1.136 30
3.2.1.139 67
3.2.1.140 20 136
3.2.1.141 13
3.2.1.145 43
3.2.1.146 2 5 43 182
3.2.1.147 1
3.2.1.149 5
3.2.1.150 5 74
3.2.1.151 5 9 12 16 26 44 45 74
3.2.1.152 2
3.2.1.153 32
3.2.1.154 32
3.2.1.156 8 10 30
3.2.1.157 82
3.2.1.158 96
3.2.1.159 117
3.2.1.161 1
3.2.1.162 150
3.2.1.163 125
3.2.1.164 30
3.2.1.165 2 9 35
3.2.1.166 79
3.2.1.167 30
3.2.1.168 5 55
3.2.1.169 84
3.2.1.170 63
3.2.1.171 28
3.2.1.172 105
3.2.1.173 28 138
3.2.1.174 78
3.2.1.175 1 17
3.2.1.176 7 48
3.2.1.177 31
3.2.1.178 16
3.2.1.179 88
3.2.1.180 88
3.2.1.181 16
3.2.1.182 1
3.2.1.185 127 142 143 146
3.2.1.187 121
3.2.1.188 1
3.2.1.197 130
3.2.1.199 31
3.2.1.200 18
3.2.1.201 18 19
3.2.1.204 31
3.2.1.205 15
3.2.1.206 1
3.2.1.208 63
3.2.1.211 107 168 174
3.2.1.212 107
3.2.1.213 30
3.2.1.216 65
3.2.1.217 31
4.2.1.179 172
4.2.2.n1 23 102 103 104
4.2.2.13 31
4.2.2.15 33
4.2.2.16 32
4.2.2.17 91
4.2.2.18 91
5.4.99.11 13
5.4.99.15 13
5.4.99.16 13

Note

Some glycoside hydrolases are multifunctional enzymes that contain catalytic domains that belong to different GH families.

Footnotes

[1] Henrissat B (1991) A classification of glycosyl hydrolases based on amino-acid sequence similarities. Biochem. J. 280:309-316 [PMID: 1747104].

[2] Henrissat B, Bairoch A (1993) New families in the classification of glycosyl hydrolases based on amino- acid sequence similarities. Biochem. J. 293:781-788 [PMID: 8352747].

[3] Henrissat B, Bairoch A (1996) Updating the sequence-based classification of glycosyl hydrolases. Biochem. J. 316:695-696 [PMID: 8687420].

[4] Davies G, Henrissat B (1995) Structures and mechanisms of glycosyl hydrolases. Structure 3:853-859 [PMID: 8535779].

[5] Terwisscha van Scheltinga A, Armand S, Kalk KH, Isogai A, Henrissat B, Dijkstra BW (1995) Stereochemistry of chitin hydrolysis by a plant chitinase/lysozyme and x-ray structure of a complex with allosamidin. Evidence for substrate assisted catalysis. Biochemistry 34:15619-15623
[PMID: 7495789].

[6] Rajan SS, Yang X, Collart F, Yip VL, Withers SG, Varrot A, Thompson J, Davies GJ, Anderson WF (2004) Novel catalytic mechanism of glycoside hydrolysis based on the structure of an NAD+/Mn2+ -dependent phospho-alpha-glucosidase from Bacillus subtilis. Structure. 12:1619-1629
[PMID: 15341727].

[7] Liu QP, Sulzenbacher G, Yuan H, Bennett EP, Pietz G, Saunders K, Spence J, Nudelman E, Levery SB, White T, Neveu JM, Lane WS, Bourne Y, Olsson ML, Henrissat B, Clausen H (2007) Bacterial glycosidases for the production of universal red blood cells. Nature Biotechnol. 25:454-464
[PMID: 17401360].

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