6AG0

The X-ray Crystallographic Structure of Maltooligosaccharide-forming Amylase from Bacillus stearothermophilus STB04


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 

wwPDB Validation 3D Report Full Report



Literature

Crystal structure of a maltooligosaccharide-forming amylase from Bacillus stearothermophilus STB04.

Xie, X.Li, Y.Ban, X.Zhang, Z.Gu, Z.Li, C.Hong, Y.Cheng, L.Jin, T.Li, Z.

(2019) Int J Biol Macromol 138: 394-402

  • DOI: 10.1016/j.ijbiomac.2019.07.104
  • Primary Citation of Related Structures:  
    6AG0

  • PubMed Abstract: 
  • To better understand structure-function relationships, an X-ray crystal structure of the maltooligosaccharide-forming amylase from Bacillus stearothermophilus STB04 (Bst-MFA) with bound acarbose has been determined at 2.2 Å. The structure revealed a ...

    To better understand structure-function relationships, an X-ray crystal structure of the maltooligosaccharide-forming amylase from Bacillus stearothermophilus STB04 (Bst-MFA) with bound acarbose has been determined at 2.2 Å. The structure revealed a classical three-domain fold stabilized by four calcium ions, in which CaI-CaIII form an unprecedented linear metal triad in the interior of domain B. Catalytic residues are deduced to be two aspartic acids and one glutamic acid (Asp234, Glu264, Asp331), and the acarbose is bound to surrounding amino acid residues, mainly through extensive hydrogen bonds. Furthermore, analysis of the structure indicates the existence of at least 8 subsites in Bst-MFA, six glycone sites (-6, -5, -4, -3, -2, -1) and two aglycone sites (+1, +2). Subsite +3 remains to be further explored. Sugar-binding subsites contribute to further presentation of the oligosaccharide-binding mode, which explains the product specificity of Bst-MFA to some extent. In addition, we propose a mechanism by which maltooligosaccharide-forming amylases produce particular maltooligosaccharide products, a result different from that seen with typical α-amylases. Finally, the three-dimensional structure of Bst-MFA complexed with acarbose provides the basis for further studies, designed to increase product specificity.


    Organizational Affiliation

    State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China. Electronic address: zfli@jiangnan.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-amylaseAC542Geobacillus stearothermophilusMutation(s): 0 
EC: 3.2.1.1
Find proteins for Q9KWY6 (Geobacillus stearothermophilus)
Explore Q9KWY6 
Go to UniProtKB:  Q9KWY6
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B, D, E, F, G, H, I, J, K, L, M
3 N/A N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.87α = 90
b = 81.82β = 105.85
c = 88.78γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31722040
National Natural Science Foundation of ChinaChina31571882

Revision History 

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2019-05-29
    Changes: Data collection, Structure summary
  • Version 1.2: 2020-04-15
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary