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PDBsum entry 2f6d

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protein ligands metals links
Hydrolase PDB id
2f6d
Jmol
Contents
Protein chain
492 a.a. *
Ligands
ACR ×2
PO4
Metals
_NA ×2
Waters ×810
* Residue conservation analysis
PDB id:
2f6d
Name: Hydrolase
Title: Structure of the complex of a glucoamylase from saccharomyco 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.Wi
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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P08017  (AMYG_SACFI) -  Glucoamylase GLU1
Seq:
Struc:
519 a.a.
492 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.3  - Glucan 1,4-alpha-glucosidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      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.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21152915 J.Marín-Navarro, and J.Polaina (2011).
Glucoamylases: structural and biotechnological aspects.
  Appl Microbiol Biotechnol, 89, 1267-1273.  
21261814 S.Cuyvers, E.Dornez, M.N.Rezaei, A.Pollet, J.A.Delcour, and C.M.Courtin (2011).
Secondary substrate binding strongly affects activity and binding affinity of Bacillus subtilis and Aspergillus niger GH11 xylanases.
  FEBS J, 278, 1098-1111.  
20552260 E.Hostinová, S.Janecek, and J.Gasperík (2010).
Gene sequence, bioinformatics and enzymatic characterization of alpha-amylase from Saccharomycopsis fibuligera KZ.
  Protein J, 29, 355-364.  
20159465 N.M.Koropatkin, and T.J.Smith (2010).
SusG: a unique cell-membrane-associated alpha-amylase from a prominent human gut symbiont targets complex starch molecules.
  Structure, 18, 200-215.
PDB codes: 3k8k 3k8l 3k8m
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