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Carbohydrate-binding modules (CBM) have been classified into more than 40 families according to sequence homology [E1]. Several amylolytic enzymes share a conserved region of 90-130 amino acid residues, the CBM20 domain. It is mainly found C-terminal to the catalytic domain and has been shown to bind granular starch [1,2].

The crystal structure of CBM20 has been solved (see <PDB:1CGT>) [3]. It consists of seven β-stands forming an open-sided distorted β-barrel. Several aromatics, especially the well-conserved Trp and Tyr residues, participates in granular starch binding. Starch consists of glucose units mainly in the form of amylose and amylopectin, which are arranged in semicrystalline arrays of double-helical strands to form large irregular granules. The two starch strands are bound to the CBM20 domain in a perpendicular orientation. This may be functionally important, as it may force starch strands apart thus increasing the hydrolyzable surface [4].

Some proteins known to contain a CBM20 domain are listed below:

• Mammalian genethonin 1 protein.
• Mammalian laforin protein, a dual specificity protein phosphatase that may be involved in the control of glycogen metabolism.
• Human hypothetical protein KIAA1434.
• Fungi glucoamylase (EC 3.2.1.3).
• Bacterial cyclomaltodextrin glucanotransferase (EC 2.4.1.19).
• Bacterial α-amylase (EC 3.2.1.1).
• Pseudomonas glucan 1,4-α-maltotetraohydrolase precursor (EC 3.2.1.60).
• Thermoanaerobacterium amylopullulanase (α-amylase/pullulanase).
• Bacillus maltogenic α-amylase (EC 3.2.1.133).

The profile we developed covers the whole CBM20 domain.

The CBM20 domain is also known as the starch-binding domain.

November 2005 / First entry.

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

CBM20, PS51166; CBM20 (carbohydrate binding type-20) 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 PS51166 • 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 PS51166 • Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS51166 • Scan Swiss-Prot/TrEMBL entries against PS51166 • view ligand binding statistics

Matching PDB structures: 1A47 1AC0 1ACZ 1B90 ... [ALL]

1	Authors	Goto M., Semimaru T., Furukawa K., Hayashida S.
	Title	Analysis of the raw starch-binding domain by mutation of a glucoamylase from Aspergillus awamori var. kawachi expressed in Saccharomyces cerevisiae.
	Source	Appl. Environ. Microbiol. 60:3926-3930(1994).
	PubMed ID	7993082

2	Authors	Chen L., Coutinho P.M., Nikolov Z., Ford C.
	Title	Deletion analysis of the starch-binding domain of Aspergillus glucoamylase.
	Source	Protein Eng. 8:1049-1055(1995).
	PubMed ID	8771186

3	Authors	Klein C., Schulz G.E.
	Title	Structure of cyclodextrin glycosyltransferase refined at 2.0 A resolution.
	Source	J. Mol. Biol. 217:737-750(1991).
	PubMed ID	1826034

4	Authors	Sorimachi K., Le Gal-Coeffet M.F., Williamson G., Archer D.B., Williamson M.P.
	Title	Solution structure of the granular starch binding domain of Aspergillus niger glucoamylase bound to beta-cyclodextrin.
	Source	Structure 5:647-661(1997).
	PubMed ID	9195884

E1
Source	http://www.cazy.org/fam/CBM20.html

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