Journal of Protein Chemistry

, Volume 12, Issue 6, pp 791-805

First online:

Starch- and glycogen-debranching and branching enzymes: Prediction of structural features of the catalytic (β/α)8-barrel domain and evolutionary relationship to other amylolytic enzymes

  • Hans M. JespersenAffiliated withDepartment of Chemistry, Carlsberg Laboratory
  • , E. Ann MacGregorAffiliated withDepartment of Chemistry, University of Manitoba
  • , Bernard HenrissatAffiliated withCentre de Recherches sur les Macromolécules Végétales, C. N. R. S., B.P.
  • , Michael R. SierksAffiliated withDepartment of Chemistry, Carlsberg Laboratory
  • , Birte SvenssonAffiliated withDepartment of Chemistry, Carlsberg Laboratory

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Sequence alignment and structure prediction are used to locate catalytic α-amylase-type (β/α)8-barrel domains and the positions of their β-strands and α-helices in isoamylase, pullulanase, neopullulanase, α-amylase-pullulanase, dextran glucosidase, branching enzyme, and glycogen branching enzymes—all enzymes involved in hydrolysis or synthesis of α-1,6-glucosidic linkages in starch and related polysaccharides. This has allowed identification of the transferase active site of the glycogen debranching enzyme and the locations of β ⇑ α loops making up the active sites of all enzymes studied. Activity and specificity of the enzymes are discussed in terms of conserved amino acid residues and loop variations. An evolutionary distance tree of 47 amylolytic and related enzymes is built on 37 residues representing the four best conserved β-strands of the barrel. It exhibits clusters of enzymes close in specificity, with the branching and glycogen debranching enzymes being the most distantly related.

Key words

α-1,6-Glucosidic bond metabolism amylolytic enzymes structure prediction sequence comparison evolutionary tree