Carbohydrate-Binding Module family classification

Introduction

A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity . A few exceptions are CBMs in cellulosomal scaffoldin proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins.

CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [1] [2]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology.

Family classification

Previous classification of cellulose-binding domains were based on amino acid similarity [3]. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII [3]. For a detailed review on the structure and binding modes of CBMs see [4].

The family classification of CBMs is expected to:

1. aid in the identification of CBMs

2. in some cases, predict binding specificity

3. aid in identifying functional residues

4. reveal evolutionary relationships

5. be predictive of polypeptide folds

The CAZy database provides an updated list of the CBM-containing proteins, arranged by CBM family. When a protein contains CBMs from different families, it appears in each appropriate family. Because the fold of proteins is better conserved than their sequences, some of the CBM families can be grouped into superfamilies or clans.

Tables for Direct Access

- CBM Family Number

12345678910111213141516171819202122232425262728293031323334353637383940
41424344454647484950515253545556575859606162636465666768697071
Non-Classified Sequences

- CBM Classification Statistics

Modules in present families 44303
Non-Classified modules 230

- EC Activities found in CBM families

Caution : Because of the modular nature of CAZymes, these activities may not be directly associated with the family but simply borne by adjacent modules.

1.-.-.- 1 2 10 20
1.1.3.9 32
1.1.99.18 1
2.4.1.- 18 20 25 35 38 40 43 61
2.4.1.18 48
2.4.1.19 20
2.4.1.21 53
2.4.1.25 20 48 68
2.4.1.41 13
2.4.1.248 35
2.4.2.- 22
3.1.1.- 1 2 12 35
3.1.1.6 2
3.1.1.72 1 2 6 22 37 NC
3.1.1.73 1 2 6 13 22 35
3.1.3.16 21
3.2.1.- 1 2 3 4 5 6 9 12 13 16 18 20 22 25 26 32 41 42 47 48 50 51 62
3.2.1.1 20 21 25 26 34 41 45 48 58 69
3.2.1.2 20 25
3.2.1.3 20 21
3.2.1.4 1 2 3 4 5 6 8 10 11 17 28 30 32 35 44 46 49 63 65 NC
3.2.1.6 4 6 13 32 54
3.2.1.8 1 2 3 4 5 6 9 10 13 15 22 35 36 37 49 59 60 64 NC
3.2.1.11 35 61
3.2.1.14 1 2 5 6 12 13 14 16 18 19 50 54 55
3.2.1.17 5 50
3.2.1.18 32 40
3.2.1.20 34
3.2.1.21 1
3.2.1.22 6 13 35
3.2.1.23 6 32 71
3.2.1.26 38
3.2.1.32 13 31 NC
3.2.1.33 48 68
3.2.1.35 32
3.2.1.37 6 22 42
3.2.1.39 4 6 13 18 32 43 52 54 56
3.2.1.40 67
3.2.1.41 20 25 34 41 48 68
3.2.1.49 13
3.2.1.50 32
3.2.1.52 32
3.2.1.54 20 34 48 58
3.2.1.55 1 2 3 6 13 22 35 36 42 NC
3.2.1.58 1
3.2.1.59 24 32 35
3.2.1.60 20 25 26
3.2.1.65 66
3.2.1.68 41 48
3.2.1.73 1 2 4 6 11 13 22 32 39 49 54
3.2.1.74 2 6 10
3.2.1.78 1 2 3 5 10 16 23 27 32 35 59 NC
3.2.1.80 38 66
3.2.1.81 6 13
3.2.1.83 16
3.2.1.88 13 35 NC
3.2.1.89 61
3.2.1.91 1 2 3 4 5 10
3.2.1.94 35
3.2.1.96 32 50
3.2.1.97 32 51
3.2.1.98 25 26
3.2.1.101 6
3.2.1.103 16
3.2.1.113 32
3.2.1.116 20
3.2.1.120 6
3.2.1.132 1 5 32
3.2.1.133 20 34 48
3.2.1.135 34 58
3.2.1.136 35
3.2.1.140 32
3.2.1.141 48
3.2.1.145 13 35
3.2.1.151 1 2 3 30 35 44 NC
3.2.1.158 6
3.2.1.165 35
3.2.1.176 1 2 3
3.2.1.178 13
4.2.2.- 2 16
4.2.2.n1 50
4.2.2.1 70
4.2.2.2 2 13 35
4.2.2.3 13 16 32
4.2.2.10 1
4.2.2.11 16 32

Footnotes

[1 Tomme, P., Van Tilbeurgh, H., Pettersson, G., Van Damme, J., Vandekerckhove, J., Knowles, J., Teeri, T. & Claeyssens, M. (1988) Studies of the cellulolytic system of Trichoderma reesei QM 9414. Analysis of domain function in two cellobiohydrolases by limited proteolysis. Eur. J. Biochem. 170, 575-581 [PMID: 3338453].

[2 Gilkes, N.R., Warren, R.A., Miller, R.C.J. & Kilburn, D.G. (1988) Precise excision of the cellulose binding domains from two Cellulomonas fimi cellulases by a homologous protease and the effect on catalysis. J. Biol. Chem. 263, 10401-10407 [PMID: 3134347].

[3 Tomme, P., Warren, R.A., Miller, R.C., Jr., Kilburn, D.G. & Gilkes, N.R. (1995) in Enzymatic Degradation of Insoluble Polysaccharides (Saddler, J.N. & Penner, M., eds.), Cellulose-binding domains: classification and properties. pp. 142-163, American Chemical Society, Washington.

[4Boraston, A.B., Bolam, D.N., Gilbert, H.J. & G.J. Davies (2004). Carbohydrate-binding modules: fine tuning polysaccharide recognition. Biochem. J. 382, 769-81 [PMID: 15214846].

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