PROSITE documentation PDOC51175CBM6 (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.
Note:The CBM6 domain is also known as cellulose-binding domain family VI (CBD VI).
Last update:December 2005 / First entry.
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PROSITE method (with tools and information) covered by this documentation:
| 1 | Authors | van Bueren A.L. Morland C. Gilbert H.J. Boraston A.B. |
| Title | Family 6 carbohydrate binding modules recognize the non-reducing end of beta-1,3-linked glucans by presenting a unique ligand binding surface. | |
| Source | J. Biol. Chem. 280:530-537(2005). | |
| PubMed ID | 15501830 | |
| DOI | 10.1074/jbc.M410113200 |
| 2 | Authors | Henshaw J.L. Bolam D.N. Pires V.M.R. Czjzek M. Henrissat B. Ferreira L.M.A. Fontes C.M.G.A. Gilbert H.J. |
| Title | The family 6 carbohydrate binding module CmCBM6-2 contains two ligand-binding sites with distinct specificities. | |
| Source | J. Biol. Chem. 279:21552-21559(2004). | |
| PubMed ID | 15004011 | |
| DOI | 10.1074/jbc.M401620200 |
| 3 | Authors | Pires V.M.R. Henshaw J.L. Prates J.A.M. Bolam D.N. Ferreira L.M.A. Fontes C.M.G.A. Henrissat B. Planas A. Gilbert H.J. Czjzek M. |
| Title | The crystal structure of the family 6 carbohydrate binding module from Cellvibrio mixtus endoglucanase 5a in complex with oligosaccharides reveals two distinct binding sites with different ligand specificities. | |
| Source | J. Biol. Chem. 279:21560-21568(2004). | |
| PubMed ID | 15010454 | |
| DOI | 10.1074/jbc.M401599200 |
| 4 | Authors | Czjzek M. Bolam D.N. Mosbah A. Allouch J. Fontes C.M.G.A. Ferreira L.M.A. Bornet O. Zamboni V. Darbon H. Smith N.L. Black G.W. Henrissat B. Gilbert H.J. |
| Title | The location of the ligand-binding site of carbohydrate-binding modules that have evolved from a common sequence is not conserved. | |
| Source | J. Biol. Chem. 276:48580-48587(2001). | |
| PubMed ID | 11673472 | |
| DOI | 10.1074/jbc.M109142200 |
| E1 | Title | https://www.cazy.org/CBM6.html |
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