PROSITE documentation PDOC51175

CBM6 (carbohydrate binding type-6) domain profile

Carbohydrate-binding modules (CBM) have been classified into more than 40 families according to sequence homology [E1]. Several cellulolytic enzymes share a conserved region of about 120 amino acid residues, the CBM6 domain [1]. The CBM6 domain is distinct from others CBMs in that this protein module contains multiple distinct ligand binding sites. CBM6 domains bind to amorphous cellulose, xylan, mixed β-(1,3)(1,4)glucan and β-1,3-glucan [1,2,3].

The CBM6 domain is mainly found C-terminal to the catalytic domain, which corresponds to a wide range of bacterial glycosyl hydrolases such as family 16 (see <PDOC00794>), or family 10 (see <PDOC00510>).

The crystal structure of CBM6 domain has been solved (see <PDB:1GMM>) [4]. It adopts a classic lectin-like β-jelly roll fold, predominantly consisting of five antiparallel β-strands on one face and four antiparallel β-strands on the other face. It contains two potential ligand binding sites, named respectively cleft A and B. These clefts include aromatic residues which are probably involved in the substrate binding. The cleft B is located on the concave surface of one β-sheet, and the cleft A on one edge of the protein between the loop that connects the inner and outer β-sheets of the jelly roll fold [4]. The multiple binding clefts confer the extensive range of specificities displayed by the domain [1,2,3].

Some proteins known to contain a CBM6 domain are listed below:

• The bacterial Endo-1,4-β-xylanase A, B, C, E, J, U, V, Y and Z (xynA, xynB, xynC, xynE, xynJ, xynU, xynV, xynY, and xynZ). They are involved in the endohydrolysis of 1,4-β-D-xylosidic linkages in xylans (EC 3.2.1.8 and EC 3.2.1.55).
• The Piromyces sp. Mannan endo-1,4-β-mannosidase A (manA) (EC 3.2.1.78).

The profile we developed covers the whole CBM6 domain.