a-Amylase

Family Ties

a-Amylase belongs to the glycosyl hydrolase 13 family of enzymes (EC 3.2.1.- and EC 2.4.1.-), a large group of enzymes that act to hydrolyse the glycosidic bonds between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. The classification of these enzymes from CAZy (Carbohydrate-Active EnZymes) lists 85 different families based on sequence similarity. In addition to a-amylase, family 13 of glycosyl hydrolases includes a enzymes with a variety of known activities: pullulanase (EC 3.2.1.41), cyclomaltodextrin glucanotransferase (EC 2.4.1.19), cyclomaltodextrinase (EC 3.2.1.54), trehalose-6-phosphate hydrolase (EC 3.2.1.93), a-glucosidase (EC 3.2.1.20), isoamylase (EC 3.2.1.68), and amylosucrase (EC 2.4.1.4), amongst others. These enzymes use an aspartic acid residue as the catalytic nucleophile/base, and a glutamic acid residue as the catalytic proton donor.

What InterPro Tells Us

P04746 Human pancreatic a-amylase

InterPro Domain Architecture

InterPro Entry	Signatures	Graphical Match	Method Name
IPR006046	PR00110		ALPHAAMYLASE
IPR006047	PF00128		Alpha-amylase
IPR006048	PF02806		Alpha-amylase_C
IPR006048	SM00632		Aamy_C
IPR006589	SM00642		Aamy
Structural Features
1hny	1hny
2.60.40.1180.1	1kbbA2
3.20.20.80.8	1kbbA1
b.71.1.1	d1hny_1
c.1.8.1	d1hny_2

From the graphical match above, you can see that the signatures are grouped into four InterPro entries for human pancreatic a-amylase. These entries give information about the domain architecture of the protein, as well as its family relationships.

To look at the family relationships, we need to consider entry IPR006046, which represents family 13 of glycosyl hydrolases, and which has one signatures: PR00110 from the PRINTS database.

The domain architecture of human pancreatic a-amylase consists of two domains, an N-terminal (beta/alpha) barrel catalytic domain (subdomains A and B), and a C-terminal all-beta barrel domain with a Greek key topology (domain C). The catalytic domain contains the active site residues, and is interrupted by a 70 amino acid calcium-binding domain that protrudes between b-strand 3 and a-helix 3. IPR006047 represents the catalytic domain found in a-amylase and in other family 13 glycosyl hydrolases. And is represented by one signature, PF00128 from the PFAM database. IPR006589 also represents the a-amylase catalytic domain, but this signature is found in fewer family members; this entry is represented by one signature, SM00642 from the SMART database. The C-terminal all-beta barrel domain is represented by IPR006048, which has two signatures: PF02806 from the PFAM database, and SM00632 from the SMART database.

The remaining five entries in the table above give information on the structure of this protein, presenting known structural data from the structural database PDB (green stripe) and the structural classification databases CATH (pink stripe) and SCOP (black stripe) (the names such as 1kbbA1 are derived from the PDB entry upon which they are based, here PDB entry 1kbb, chain A, fragment 1). The graphical match for the PDB entry 1hny displays the full length of the original PDB entry, here covering almost the entire protein. The CATH and SCOP entries breakdown the PDB data into its constituent domains and provide a structural classification for each domain: the N-terminal catalytic domain (SCOP d1hny_2 and CATH 1kbbA1 both classed as a + b), and the C-terminal domain (SCOP d1hny_1 and CATH 1kbbA2 both classed as all b).

What the Structure Tells Us

Structures associated with human a-amylases can be viewed using AstexViewer®, which is linked from the Match Table via the logo on the InterPro page (please note, there is no link directly from this page to the AstexViewer®, therefore you need to go to the link on the InterPro page for P04746). The AstexViewer® displays the PDB structure with the specific CATH or SCOP domain highlighted.

There are structures available for amylases from several different species in the Protein Data Bank (PDB). A detailed description and visualisation of the structural features of amylases can be found at the PDB ‘Molecule of the Month’. The crystallographic structures of different amylases have provided insight into the mechanism of action of these important enzymes.

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