1UA7 | pdb_00001ua7

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

PDB DOI: https://doi.org/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free:
0.265 (Depositor), 0.260 (DCC)
R-Value Work:
0.208 (Depositor), 0.200 (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

PubMed: 14617662 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/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.

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
Modelled Residue Count: 422
Deposited Residue Count: 422
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00691
Sequence Annotations Expand
Reference Sequence LOADING

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
4,6-dideoxy-alpha-D-xylo-hexopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G59234JH GlyCosmos: G59234JH

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACI Query on ACI Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL C₇ H₁₃ N O₄ XPHOBMULWMGEBA-VZFHVOOUSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	F [auth A], G [auth A], H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.265 (Depositor), 0.260 (DCC)
R-Value Work: 0.208 (Depositor), 0.200 (DCC)
R-Value Observed: 0.208 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2004-05-18

Deposition Author(s):

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