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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 150 amino acid residues, the CBM3 domain [1]. It has been classified in three different subtypes, termed family IIIa, IIIb and IIIc. The family IIIa (scaffoldin) and IIIb (mainly free enzymes) are closely similar in their primary structures and both types bind strongly to crystalline cellulose [2,3]. Members of the family IIIc, fails to bind crystalline cellulose, but serves in a 'helper' capacity by feeding a single incoming cellulose chain into the active site of the neighbouring catalytic module pending hydrolysis [4,5].

The CBM3 domain is mainly found C-terminal to the catalytic domain, which correspond to a wide range of bacterial glycosyl hydrolases like family 9 (see <PDOC00511>), family 5 (see <PDOC00565>) and family 10 (see <PDOC00510>).

The crystal structure of CBM3 has been solved (see <PDB:1NBC>) [2]. It consists of nine β-strands which form a compact domain that has an overall prismatic shape. It is arranged in two antiparallel β-sheets that stack face-to-face to form a β sandwich with jelly roll topology. Two defined surfaces, located on opposite sides of the molecule, contain conserved polar and aromatic residues which are probably involved in the binding of the CBM to cellulose [2,3]. The first one forms a planar strip whereas the second one forms a shallow groove.

Some proteins known to contain a CBM3 domain are listed below:

• Clostridial cellulosomal scaffolding proteins cipA, cipC and cbpA. They promote the binding of cellulose to the catalytic domains of the cellulolytic enzymes.
• Bacterial cellulases A, B, F, G, I, N, Y, Z (Endo-1,4-β-glucanase) (EC 3.2.1.4).

The profile we developed covers the whole CBM3 domain.

The CBM3 domain is also known as cellulose-binding domain family III (CBD III).

December 2005 / First entry.

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

CBM3, PS51172; CBM3 (carbohydrate binding type-3) 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 PS51172 • 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 PS51172 • Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS51172 • Scan Swiss-Prot/TrEMBL entries against PS51172 • view ligand binding statistics

Matching PDB structures: 1G87 1GA2 1JS4 1K72 ... [ALL]

1	Authors	Poole D.M., Morag E., Lamed R., Bayer E.A., Hazlewood G.P., Gilbert H.J.
	Title	Identification of the cellulose-binding domain of the cellulosome subunit S1 from Clostridium thermocellum YS.
	Source	FEMS Microbiol. Lett. 78:181-186(1992).
	PubMed ID	1490597

2	Authors	Tormo J., Lamed R., Chirino A.J., Morag E., Bayer E.A., Shoham Y., Steitz T.A.
	Title	Crystal structure of a bacterial family-III cellulose-binding domain: a general mechanism for attachment to cellulose.
	Source	EMBO J. 15:5739-5751(1996).
	PubMed ID	8918451

3	Authors	Shimon L.J.W., Pages S., Belaich A., Belaich J.-P., Bayer E.A., Lamed R., Shoham Y., Frolow F.
	Title	Structure of a family IIIa scaffoldin CBD from the cellulosome of Clostridium cellulolyticum at 2.2 A resolution.
	Source	Acta Crystallogr. D 56:1560-1568(2000).
	PubMed ID	11092922

4	Authors	Irwin D., Shin D.-H., Zhang S., Barr B.K., Sakon J., Karplus P.A., Wilson D.B.
	Title	Roles of the catalytic domain and two cellulose binding domains of Thermomonospora fusca E4 in cellulose hydrolysis.
	Source	J. Bacteriol. 180:1709-1714(1998).
	PubMed ID	9537366

5	Authors	Gal L., Pages S., Gaudin C., Belaich A., Reverbel-Leroy C., Tardif C., Belaich J.-P.
	Title	Characterization of the cellulolytic complex (cellulosome) produced by Clostridium cellulolyticum.
	Source	Appl. Environ. Microbiol. 63:903-909(1997).
	PubMed ID	9055408

E1
Source	http://www.cazy.org/fam/CBM3.html

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