1BFN

BETA-AMYLASE/BETA-CYCLODEXTRIN COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 

wwPDB Validation 3D Report Full Report



Literature

Crystal structure of recombinant soybean beta-amylase complexed with beta-cyclodextrin.

Adachi, M.Mikami, B.Katsube, T.Utsumi, S.

(1998) J Biol Chem 273: 19859-19865

  • DOI: 10.1074/jbc.273.31.19859
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In order to study the interaction of soybean beta-amylase with substrate, we solved the crystal structure of beta-cyclodextrin-enzyme complex and compared it with that of alpha-cyclodextrin-enzyme complex. The enzyme was expressed in Escherichia coli at a high level as a soluble and catalytically active protein ...

    In order to study the interaction of soybean beta-amylase with substrate, we solved the crystal structure of beta-cyclodextrin-enzyme complex and compared it with that of alpha-cyclodextrin-enzyme complex. The enzyme was expressed in Escherichia coli at a high level as a soluble and catalytically active protein. The purified recombinant enzyme had properties nearly identical to those of native soybean beta-amylase and formed the same crystals as the native enzyme. The crystal structure of recombinant enzyme complexed with beta-cyclodextrin was refined at 2. 07-A resolution with a final crystallographic R value of 15.8% (Rfree = 21.1%). The root mean square deviation in the position of C-alpha atoms between this recombinant enzyme and the native enzyme was 0.22 A. These results indicate that the expression system established here is suitable for studying structure-function relationships of beta-amylase. The conformation of the bound beta-cyclodextrin takes an ellipsoid shape in contrast to the circular shape of the bound alpha-cyclodextrin. The cyclodextrins shared mainly two glucose binding sites, 3 and 4. The glucose residue 4 was slightly shifted from the maltose binding site. This suggests that the binding site of the cyclodextrins is important for its holding of a cleaved substrate, which enables the multiple attack mechanism of beta-amylase.


    Related Citations: 
    • Crystal Structures of Soybean Beta-Amylase Reacted with Beta-Maltose and Maltal: Active Site Components and Their Apparent Roles in Catalysis
      Mikami, B., Degano, M., Hehre, E.J., Sacchettini, J.C.
      (1994) Biochemistry 33: 7779
    • The 2.0-A Resolution Structure of Soybean Beta-Amylase Complexed with Alpha-Cyclodextrin
      Mikami, B., Hehre, E.J., Sato, M., Katsube, Y., Hirose, M., Morita, Y., Sacchettini, J.C.
      (1993) Biochemistry 32: 6836

    Organizational Affiliation

    Research Institute for Food Science, Kyoto University, Uji Kyoto 611-0011, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-AMYLASEA495Glycine maxMutation(s): 2 
Gene Names: BMY1
EC: 3.2.1.2
Find proteins for P10538 (Glycine max)
Explore P10538 
Go to UniProtKB:  P10538
Protein Feature View
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  • Reference Sequence
Oligosaccharides
Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
Cycloheptakis-(1-4)-(alpha-D-glucopyranose)
N/A
7 N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.03α = 90
b = 86.03β = 90
c = 144.8γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-28
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Structure summary