PROSITE documentation PDOC00485

CBM2 (carbohydrate-binding type-2) domain signature and profile

The microbial degradation of cellulose and xylans requires several types of enzyme such as endoglucanases (EC 3.2.1.4), cellobiohydrolases (EC 3.2.1.91) (exoglucanases), or xylanases (EC 3.2.1.8) [1]. Structurally, cellulases and xylanases generally consist of a catalytic domain and a conserved region of ~100 amino acid residues, the carbohydrate-binding module 2 (CBM2) [2,E1]. It is found either at the N-terminal or at the C-terminal extremity of these enzymes.

CBM2 can be classified in 2 subfamilies according to substrate specificities: CBM2a which binds cellulose and CBM2b which interacts specifically with xylan. CBM2a and CBM2b also display significant differences at the residue level as shown in the following schematic representation:

           +-------------------------------------------------+
           |                                                 |
 CBM2a    xCxxxxWxxGxxNxxxxxxxxxxxWxxxxxxxxWNxxxxxGxxxxxxxxxxCx
                                           ********

           +-------------------------------------------------+
           |                                                 |
 CBM2b    xCxxxxWxxRxxNxxxxxxxxxxxWxxxxxxx--------GxxxxxxxxxxCx

'C': conserved cysteine involved in a disulfide bond.
'*': position of the pattern.
'W': surface-exposed tryptophan

Like other CBM domains CBM2 is a β-sheet domain containing a planar face which interacts with its ligand via a hydrophobic strip of aromatic residues (see <PDB:1EXG>) [3]. In family 2a this hydrophobic surface consists of three tryptophan residues, which are all required for binding soluble and insoluble forms of cellulose [4]. In family 2b only 2 surface-exposed tryptophans are conserved and the first one is oriented differently. It is therefore not well oriented to interact with cellulose but is ideal for binding xylan [5].

Enzymes known to contain such a domain are:

• Endoglucanase (gene end1) from Butyrivibrio fibrisolvens.
• Endoglucanases A (gene cenA) and B (cenB) from Cellulomonas fimi.
• Exoglucanases A (gene cbhA) and B (cbhB) from Cellulomonas fimi.
• Endoglucanase E-2 (gene celB) from Thermomonospora fusca.
• Endoglucanase A (gene celA) from Microbispora bispora.
• Endoglucanases A (gene celA), B (celB) and C (celC) from Pseudomonas fluorescens.
• Endoglucanase A (gene celA) from Streptomyces lividans.
• Exocellobiohydrolase (gene cex) from Cellulomonas fimi.
• Xylanases A (gene xynA) and B (xynB) from Pseudomonas fluorescens.
• Arabinofuranosidase C (EC 3.2.1.55) (xylanase C) (gene xynC) from Pseudomonas fluorescens.
• Chitinase 63 (EC 3.2.1.14) from Streptomyces plicatus.
• Chitinase C from Streptomyces lividans.

To recognize the CBM2a domain we developed a pattern which is located in a conserved region specific to CBM2a. We also developed a profile which covers the whole CBM2 domain and recognizes both CBM2 subfamilies.