Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 47.90 kDa 
• Atom Count: 3808 
• Modelled Residue Count: 422 
• Deposited Residue Count: 422 
• Unique protein chains: 1

1UA7

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

• PDB DOI: 10.2210/pdb1UA7/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis
• Expression System: Bacillus subtilis
• Mutation(s): Yes 


• Deposited: 2003-03-03 Released: 2004-05-18 
• Deposition Author(s): Kagawa, M., Fujimoto, Z., Momma, M., Takase, K., Mizuno, H.

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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 

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: 14617662 
• 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-amylase	A	422	Bacillus subtilis	Mutation(s): 1  EC: 3.2.1.1
UniProt
Find proteins for P00691 (Bacillus subtilis (strain 168)) Explore P00691  Go to UniProtKB:  P00691

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
4,6-dideoxy-alpha-D-xylo-hexopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G59234JH GlyCosmos:  G59234JH

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-quinovopyranose-(1-4)-beta-D-glucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan:  G40192QI GlyCosmos:  G40192QI

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACI	D [auth A], E [auth A]	6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL C7 H13 N O4 XPHOBMULWMGEBA-VZFHVOOUSA-N
CA	F [auth A], G [auth A], H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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 = 70.32	α = 90
b = 74.204	β = 90
c = 115.724	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-03-03 
• Released Date: 2004-05-18 
Deposition Author(s): Kagawa, M., Fujimoto, Z., Momma, M., Takase, K., Mizuno, H.

Revision History  

• 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