Structure of glucoamylase from Saccharomycopsis fibuligera at 1.7 A resolution

Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):854-66. doi: 10.1107/s0907444998002005.


The yeast Saccharomycopsis fibuligera produces a glucoamylase which belongs to sequence family 15 of glycosyl hydrolases. The structure of the non-glycosyl-ated recombinant enzyme has been determined by molecular replacement and refined against 1.7 A resolution synchrotron data to an R factor of 14.6%. This is the first report of the three-dimensional structure of a yeast family 15 glucoamylase. The refinement from the initial molecular-replacement model was not straightforward. It involved the use of an unrestrained automated refinement procedure (uARP) in combination with the maximum-likelihood refinement program REFMAC. The enzyme consists of 492 amino-acid residues and has 14 alpha-helices, 12 of which form an (alpha/alpha)6 barrel. It contains a single catalytic domain but no starch-binding domain. The fold of the molecule and the active site are compared to the known structure of the catalytic domain of a fungal family 15 glucoamylase and are shown to be closely similar. The active- and specificity-site residues are especially highly conserved. The model of the acarbose inhibitor from the analysis of the fungal enzyme fits tightly into the present structure. The active-site topology is a pocket and hydrolysis proceeds with inversion of the configuration at the anomeric carbon. The enzyme acts as an exo-glycosyl hydrolase. There is a Tris [2-amino-2-(hydroxymethyl)-1,3-propanediol] molecule acting as an inhibitor in the active-site pocket.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Crystallization
  • Crystallography, X-Ray
  • Fungal Proteins / chemistry*
  • Glucan 1,4-alpha-Glucosidase / chemistry*
  • Glycoside Hydrolases / chemistry
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Conformation*
  • Protein Folding
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Species Specificity
  • Yeasts / enzymology*


  • Fungal Proteins
  • Glycoside Hydrolases
  • Glucan 1,4-alpha-Glucosidase

Associated data

  • PDB/1AYX