1AYX image
Deposition Date 1997-11-12
Release Date 1998-05-13
Last Version Date 2024-02-07
Entry Detail
PDB ID:
1AYX
Keywords:
Title:
CRYSTAL STRUCTURE OF GLUCOAMYLASE FROM SACCHAROMYCOPSIS FIBULIGERA AT 1.7 ANGSTROMS
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.70 Å
R-Value Free:
0.18
R-Value Work:
0.14
R-Value Observed:
0.14
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:GLUCOAMYLASE
Gene (Uniprot):GLU1
Chain IDs:A
Chain Length:492
Number of Molecules:1
Biological Source:Saccharomycopsis fibuligera
Ligand Molecules
Primary Citation
Structure of glucoamylase from Saccharomycopsis fibuligera at 1.7 A resolution.
Acta Crystallogr.,Sect.D 54 854 866 (1998)
PMID: 9757101 DOI: 10.1107/S0907444998002005

Abstact

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.

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Primary Citation of related structures