PDBsum entry 2f6d

Hydrolase

PDB id: 2f6d

Contents

Protein chain

492 a.a. *

Ligands

GLC-GLC-AC1 ×2

PO4

Metals

_NA ×2

Waters ×810

* Residue conservation analysis

PDB id:

2f6d

Name:

Hydrolase

Title:

Structure of the complex of a glucoamylase from saccharomycopsis fibuligera with acarbose

Structure:

Glucoamylase glu1. Chain: a. Synonym: glucan 1,4-alpha-glucosidase, 1,4-alpha-d-glucan glucohydrolase. Engineered: yes

Source:

Saccharomycopsis fibuligera. Organism_taxid: 4944. Strain: hut 7212. Gene: glu1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.60Å R-factor: 0.120 R-free: 0.160

Authors:

J.Sevcik,E.Hostinova,A.Solovicova,J.Gasperik,Z.Dauter,K.S.Wilson

Key ref:

J.Sevcík et al. (2006). Structure of the complex of a yeast glucoamylase with acarbose reveals the presence of a raw starch binding site on the catalytic domain. FEBS J, 273, 2161-2171. PubMed id: 16649993 DOI: 10.1111/j.1742-4658.2006.05230.x

Date:

29-Nov-05 Release date: 23-May-06

Protein chain

P08017  (AMYG_SACFI) -  Glucoamylase GLU1 from Saccharomycopsis fibuligera

Seq: 519 a.a.

Struc: 492 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.3 - glucan 1,4-alpha-glucosidase.
• Reaction: Hydrolysis of terminal 1,4-linked alpha-D-glucose residues successively from non-reducing ends of the chains with release of beta-D-glucose.

DOI no: 10.1111/j.1742-4658.2006.05230.x

FEBS J 273:2161-2171 (2006)

PubMed id: 16649993

Structure of the complex of a yeast glucoamylase with acarbose reveals the presence of a raw starch binding site on the catalytic domain.

J.Sevcík, E.Hostinová, A.Solovicová, J.Gasperík, Z.Dauter, K.S.Wilson.

ABSTRACT

Most glucoamylases (alpha-1,4-D-glucan glucohydrolase, EC 3.2.1.3) have structures consisting of both a catalytic and a starch binding domain. The structure of a glucoamylase from Saccharomycopsis fibuligera HUT 7212 (Glu), determined a few years ago, consists of a single catalytic domain. The structure of this enzyme with the resolution extended to 1.1 A and that of the enzyme-acarbose complex at 1.6 A resolution are presented here. The structure at atomic resolution, besides its high accuracy, shows clearly the influence of cryo-cooling, which is manifested in shrinkage of the molecule and lowering the volume of the unit cell. In the structure of the complex, two acarbose molecules are bound, one at the active site and the second at a site remote from the active site, curved around Tyr464 which resembles the inhibitor molecule in the 'sugar tongs' surface binding site in the structure of barley alpha-amylase isozyme 1 complexed with a thiomalto-oligosaccharide. Based on the close similarity in sequence of glucoamylase Glu, which does not degrade raw starch, to that of glucoamylase (Glm) from S. fibuligera IFO 0111, a raw starch-degrading enzyme, it is reasonable to expect the presence of the remote starch binding site at structurally equivalent positions in both enzymes. We propose the role of this site is to fix the enzyme onto the surface of a starch granule while the active site degrades the polysaccharide. This hypothesis is verified here by the preparation of mutants of glucoamylases Glu and Glm.

Selected figure(s)

Figure 5.
Fig. 5. A space filling model showing the complex of glucoamylase with acarbose. Both acarbose molecules are in yellow. Tyr464 is in green, Asp450 in red and Arg15 in blue. The rest of residues interacting with the surface acarbose are hidden below it.

Figure 6.
Fig. 6. Stereo picture of the surface acarbose curved around Tyr464 and the interacting partners Arg15, His447, Asp450 and Thr462 drawn using MOLSCRIPT.

The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS J (2006, 273, 2161-2171) copyright 2006.

Figures were selected by an automated process.