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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.

The CBM6 domain is also known as cellulose-binding domain family VI (CBD VI).

December 2005 / First entry.

PROSITE method (with tools and information) covered by this documentation:

CBM6, PS51175; CBM6 (carbohydrate binding type-6) domain profile  (MATRIX)

Sequences known to belong to this class detected by the profile: ALL Other sequence(s) detected in Swiss-Prot: NONE.

• Domain architecture view of Swiss-Prot proteins matching PS51175 • Retrieve an alignment of Swiss-Prot true positive hits:   Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format • Retrieve the sequence logo from the alignment • Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS51175 • Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS51175 • Scan Swiss-Prot/TrEMBL entries against PS51175 • view ligand binding statistics

Matching PDB structures: 1NAE 1O8P 1O8S 1OD3 ... [ALL]

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
Source	http://www.cazy.org/fam/CBM6.html

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