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 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 3.0 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

  • DOI: 10.1128/jb.185.23.6981-6984.2003
  • Primary Citation of Related Structures:  
    1UA7

  • 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 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 ...

    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
    • 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
    • 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 96: 1849
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-amylaseA422Bacillus subtilisMutation(s): 1 
EC: 3.2.1.1
UniProt
Find proteins for P00691 (Bacillus subtilis (strain 168))
Explore P00691 
Go to UniProtKB:  P00691
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
4,6-dideoxy-alpha-D-xylo-hexopyranose-(1-4)-alpha-D-glucopyranoseB2 N/A Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-quinovopyranose-(1-4)-beta-D-glucopyranoseC2 N/A Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACI
Query on ACI
Download Ideal Coordinates CCD File 
 D [auth A], E [auth A]6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL
C7 H13 N O4
XPHOBMULWMGEBA-VZFHVOOUSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
 F [auth A], G [auth A], H [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-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 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.32α = 90
b = 74.204β = 90
c = 115.724γ = 90
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-18
    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: 2017-10-04
    Changes: Refinement description
  • Version 2.0: 2017-10-25
    Changes: Atomic model, Derived calculations, Structure summary
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary