Domain evolution in the alpha-amylase family

J Mol Evol. 1997 Sep;45(3):322-31. doi: 10.1007/pl00006236.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Amino Acids / metabolism
  • Antigens, CD / chemistry
  • Antigens, CD / genetics
  • Antigens, CD / metabolism
  • Carrier Proteins / chemistry
  • Carrier Proteins / genetics
  • Carrier Proteins / metabolism
  • Evolution, Molecular*
  • Fusion Regulatory Protein-1
  • Glycoside Hydrolases / chemistry
  • Glycoside Hydrolases / genetics
  • Glycoside Hydrolases / metabolism
  • Molecular Sequence Data
  • Sequence Alignment
  • alpha-Amylases / chemistry
  • alpha-Amylases / genetics*
  • alpha-Amylases / metabolism*


  • Amino Acids
  • Antigens, CD
  • Carrier Proteins
  • Fusion Regulatory Protein-1
  • Glycoside Hydrolases
  • alpha-Amylases