1UA7

Crystal Structure Analysis of Alpha-Amylase from Bacillus Subtilis complexed with Acarbose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Crystal structure of Bacillus subtilis alpha-amylase in complex with acarbose

Kagawa, M.Fujimoto, Z.Momma, M.Takase, K.Mizuno, H.

(2003) J.BACTERIOL. 185: 6981-6984


  • PubMed Abstract: 
  • The crystal structure of Bacillus subtilis alpha-amylase, in complex with the pseudotetrasaccharide inhibitor acarbose, revealed an hexasaccharide in the active site as a result of transglycosylation. After comparison with the known structure of the ...

    The crystal structure of Bacillus subtilis alpha-amylase, in complex with the pseudotetrasaccharide inhibitor acarbose, revealed an hexasaccharide in the active site as a result of transglycosylation. After comparison with the known structure of the catalytic-site mutant complexed with the native substrate maltopentaose, it is suggested that the present structure represents a mimic intermediate in the initial stage of the catalytic process.


    Related Citations: 
    • Crystal structure of a catalytic-site mutant alpha-amylase from Bacillus subtilis complexed with maltopentaose
      Fujimoto, Z.,Takase, K.,Doui, N.,Momma, M.,Matsumoto, T.,Mizuno, H.
      (1998) J.Mol.Biol. 277: 393
    • Site-directed mutagenesis of active site residues in Bacillus subtilis alpha-amylase
      Takase, K.,Matsumoto, T.,Mizuno, H.,Yamane, K.
      (1992) BIOCHIM.BIOPHYS.ACTA 1120: 281
    • Changes in the properties and molecular weights of Bacillus subtilis M-type and N-type alpha-amylases resulting from a spontaneous deletion
      Yamane, K.,Hirata, Y.,Furusato, T.,Yamazaki, H.,Nakayama, A.
      (1984) J.BIOCHEM.(TOKYO) 96: 1849
    • Crystallization and preliminary X-ray studies of wild type and catalytic-site mutant alpha-amylase from Bacillus subtilis
      Mizuno, H.,Morimoto, Y.,Tsukihara, T.,Matsumoto, T.,Takase, K.
      (1993) J.Mol.Biol. 234: 1282


    Organizational Affiliation

    Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-amylase
A
422Bacillus subtilis (strain 168)Gene Names: amyE (amyA)
EC: 3.2.1.1
Find proteins for P00691 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P00691
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLD
Query on GLD

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Download CCD File 
A
4,6-DIDEOXYGLUCOSE
C6 H12 O4
BJBURJZEESAQPG-MOJAZDJTSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BGC
Query on BGC

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Download CCD File 
A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
GLC
Query on GLC

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Download CCD File 
A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
ACI
Query on ACI

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Download CCD File 
A
6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL
C7 H13 N O4
XPHOBMULWMGEBA-VZFHVOOUSA-N
 Ligand Interaction
G6D
Query on G6D

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Download CCD File 
A
6-DEOXY-ALPHA-D-GLUCOSE
D-Quinovose
C6 H12 O5
SHZGCJCMOBCMKK-DVKNGEFBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.320α = 90.00
b = 74.204β = 90.00
c = 115.724γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description
  • Version 2.0: 2017-10-25
    Type: Atomic model, Derived calculations, Structure summary