1UA7 | pdb_00001ua7

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 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

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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: https://doi.org/10.1128/JB.185.23.6981-6984.2003
  • Primary Citation 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.

    • Organizational Affiliation: 
    • Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.

Macromolecule Content 

  • Total Structure Weight: 47.9 kDa 
  • Atom Count: 3,808 
  • Modeled Residue Count: 422 
  • Deposited Residue Count: 422 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-amylase422Bacillus subtilisMutation(s): 1 
EC: 3.2.1.1
UniProt
Find proteins for P00691 (Bacillus subtilis (strain 168))
Explore P00691 
Go to UniProtKB:  P00691
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00691
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
4,6-dideoxy-alpha-D-xylo-hexopyranose-(1-4)-alpha-D-glucopyranose
B
2N/A
Glycosylation Resources
GlyTouCan: G59234JH
GlyCosmos: G59234JH
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-quinovopyranose-(1-4)-beta-D-glucopyranose
C
2N/A
Glycosylation Resources
GlyTouCan: G40192QI
GlyCosmos: G40192QI
GlyGen: G40192QI

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free:  0.265 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
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

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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
  • Version 3.1: 2021-11-10
    Changes: Database references, Structure summary
  • Version 3.2: 2023-12-27
    Changes: Data collection