title: Domain evolution in the alpha-amylase family.
abstract: The available amino acid sequences of the alpha-amylase family (glycosyl hydrolase family 13) were searched to identify their domain B, a distinct domain that protrudes from the regular catalytic (beta/alpha)8-barrel between the strand beta3 and the helix alpha3. The isolated domain B sequences were inspected visually and also analyzed by Hydrophobic Cluster Analysis (HCA) to find common features. Sequence analyses and inspection of the few available three-dimensional structures suggest that the secondary structure of domain B varies with the enzyme specificity. Domain B in these different forms, however, may still have evolved from a common ancestor. The largest number of different specificities was found in the group with structural similarity to domain B from Bacillus cereus oligo-1,6-glucosidase that contains an alpha-helix succeeded by a three-stranded antiparallel beta-sheet. These enzymes are alpha-glucosidase, cyclomaltodextrinase, dextran glucosidase, trehalose-6-phosphate hydrolase, neopullulanase, and a few alpha-amylases. Domain B of this type was observed also in some mammalian proteins involved in the transport of amino acids. These proteins show remarkable similarity with (beta/alpha)8-barrel elements throughout the entire sequence of enzymes from the oligo-1, 6-glucosidase group. The transport proteins, in turn, resemble the animal 4F2 heavy-chain cell surface antigens, for which the sequences either lack domain B or contain only parts thereof. The similarities are compiled to indicate a possible route of domain evolution in the alpha-amylase family.
authors.affiliation: Institute of Microbiology, Slovak Academy of Sciences, Stefánikova 3, SK-81434 Bratislava, Slovakia.
authors.forename: S
authors.initials: S
authors.lastname: Janecek
authors.forename: B
authors.initials: B
authors.lastname: Svensson
authors.forename: B
authors.initials: B
authors.lastname: Henrissat
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000378:metabolism; D015703:Antigens, CD / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D002352:Carrier Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D019143:Evolution, Molecular; D027261:Fusion Regulatory Protein-1; D006026:Glycoside Hydrolases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D000516:alpha-Amylases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*
chemical_list: D000596:Amino Acids; D015703:Antigens, CD; D002352:Carrier Proteins; D027261:Fusion Regulatory Protein-1; D006026:Glycoside Hydrolases; D000516:alpha-Amylases