1J11

beta-amylase from Bacillus cereus var. mycoides in complex with alpha-EPG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal Structures of beta-Amylase from Bacillus cereus var. mycoides in Complexes with Substrate Analogs and Affinity-Labeling Reagents

Oyama, T.Miyake, H.Kusunoki, M.Nitta, Y.

(2003) J Biochem 133: 467-474

  • DOI: 10.1093/jb/mvg061
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structures of beta-amylase from Bacillus cereus var. mycoides in complexes with five inhibitors were solved. The inhibitors used were three substrate analogs, i.e. glucose, maltose (product), and a synthesized compound, O-alpha-D-glucopyr ...

    The crystal structures of beta-amylase from Bacillus cereus var. mycoides in complexes with five inhibitors were solved. The inhibitors used were three substrate analogs, i.e. glucose, maltose (product), and a synthesized compound, O-alpha-D-glucopyranosyl-(1-->4)-O-alpha-D-glucopyranosyl-(1-->4)-D-xylopyranose (GGX), and two affinity-labeling reagents with an epoxy alkyl group at the reducing end of glucose. For all inhibitors, one molecule was bound at the active site cleft and the non-reducing end glucose of the four inhibitors except GGX was located at subsite 1, accompanied by a large conformational change of the flexible loop (residues 93-97), which covered the bound inhibitor. In addition, another molecule of maltose or GGX was bound about 30 A away from the active site. A large movement of residues 330 and 331 around subsite 3 was also observed upon the binding of GGX at subsites 3 to 5. Two affinity-labeling reagents, alpha-EPG and alpha-EBG, were covalently bound to a catalytic residue (Glu-172). A substrate recognition mechanism for the beta-amylase was discussed based on the modes of binding of these inhibitors in the active site cleft.


    Related Citations: 
    • Crystal Structure of beta-Amylase from Bacillus cereus var. mycoides at 2.2 A resolution
      Oyama, T., Kusunoki, M., Kishimoto, Y., Takasaki, Y., Nitta, Y.
      (1999) J Biochem 125: 1120
    • Kinetic Study of Active Site Structure of beta-Amylase from Bacillus cereus var. mycoides
      Nitta, Y., Shirakawa, M., Takasaki, Y.
      (1996) Biosci Biotechnol Biochem 60: 823

    Organizational Affiliation

    Laboratory of Enzyme Chemistry, Graduate School of Agriculture and Biological Science, Osaka Prefecture University, Sakai, Osaka 599-8531. nitta@biochem.osakafu-u.ac.jp



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-amylaseA, B, C, D516Bacillus cereusMutation(s): 0 
Gene Names: spoII
EC: 3.2.1.2
Find proteins for P36924 (Bacillus cereus)
Explore P36924 
Go to UniProtKB:  P36924
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPG
Query on EPG

Download CCD File 
A, B, C, D
(2R)-oxiran-2-ylmethyl alpha-D-glucopyranoside
C9 H16 O7
NXJZWOCFSMYDAS-NZJLWHDDSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.9α = 90
b = 112.9β = 105.8
c = 146.2γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary