8IDS | pdb_00008ids

Crystal structure of Bacillus sp. AHU2216 GH13_31 Alpha-glucosidase E256Q/N258P in complex with maltotriose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.186 (Depositor), 0.186 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8IDS

This is version 1.1 of the entry. See complete history

Literature

Alteration of Substrate Specificity and Transglucosylation Activity of GH13_31 alpha-Glucosidase from Bacillus sp. AHU2216 through Site-Directed Mutagenesis of Asn258 on beta → alpha Loop 5.

Auiewiriyanukul, W.Saburi, W.Ota, T.Yu, J.Kato, K.Yao, M.Mori, H.

(2023) Molecules 28

  • DOI: https://doi.org/10.3390/molecules28073109
  • Primary Citation Related Structures: 
    8IBK, 8IDS

  • PubMed Abstract: 

    α-Glucosidase catalyzes the hydrolysis of α-d-glucosides and transglucosylation. Bacillus sp. AHU2216 α-glucosidase (BspAG13_31A), belonging to the glycoside hydrolase family 13 subfamily 31, specifically cleaves α-(1→4)-glucosidic linkages and shows high disaccharide specificity. We showed previously that the maltose moiety of maltotriose (G3) and maltotetraose (G4), covering subsites +1 and +2 of BspAG13_31A, adopts a less stable conformation than the global minimum energy conformation. This unstable d-glucosyl conformation likely arises from steric hindrance by Asn258 on β→α loop 5 of the catalytic (β/α) 8 -barrel. In this study, Asn258 mutants of BspAG13_31A were enzymatically and structurally analyzed. N258G/P mutations significantly enhanced trisaccharide specificity. The N258P mutation also enhanced the activity toward sucrose and produced erlose from sucrose through transglucosylation. N258G showed a higher specificity to transglucosylation with p -nitrophenyl α-d-glucopyranoside and maltose than the wild type. E256Q/N258G and E258Q/N258P structures in complex with G3 revealed that the maltose moiety of G3 bound at subsites +1 and +2 adopted a relaxed conformation, whereas a less stable conformation was taken in E256Q. This structural difference suggests that stabilizing the G3 conformation enhances trisaccharide specificity. The E256Q/N258G-G3 complex formed an additional hydrogen bond between Met229 and the d-glucose residue of G3 in subsite +2, and this interaction may enhance transglucosylation.


  • Organizational Affiliation
    • Research Faculty of Agriculture, Hokkaido Unifversity, Sapporo 060-8589, Japan.

Macromolecule Content 

  • Total Structure Weight: 66.57 kDa 
  • Atom Count: 5,053 
  • Modeled Residue Count: 543 
  • Deposited Residue Count: 563 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-glucosidase563Bacillus sp. (in: firmicutes)Mutation(s): 2 
Gene Names: BspAG13A
UniProt
Find proteins for A0ACD6B9E0 (Bacillus sp)
Explore A0ACD6B9E0 
Go to UniProtKB:  A0ACD6B9E0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B9E0
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseB [auth C]3N/A
Glycosylation Resources
GlyTouCan: G96370VA
GlyCosmos: G96370VA
GlyGen: G96370VA

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.186 (Depositor), 0.186 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.517α = 90
b = 89.202β = 90
c = 128.282γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-03
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Data collection