PROSITE documentation PDOC51166

CBM20 (carbohydrate binding type-20) domain profile

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.