7P01

Structure of the maltase BaAG2 from Blastobotrys adeninivorans in complex with acarbose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Insight into a Yeast Maltase-The Ba AG2 from Blastobotrys adeninivorans with Transglycosylating Activity.

Ernits, K.Kjeldsen, C.Persson, K.Grigor, E.Alamae, T.Visnapuu, T.

(2021) J Fungi (Basel) 7

  • DOI: 10.3390/jof7100816
  • Primary Citation of Related Structures:  
    7P01, 7P07

  • PubMed Abstract: 
  • An early-diverged yeast, Blastobotrys ( Arxula ) adeninivorans ( Ba ), has biotechnological potential due to nutritional versatility, temperature tolerance, and production of technologically applicable enzymes. We have biochemically characterized from the Ba type strain (CBS 8244) the GH13-family maltase Ba AG2 with efficient transglycosylation activity on maltose ...

    An early-diverged yeast, Blastobotrys ( Arxula ) adeninivorans ( Ba ), has biotechnological potential due to nutritional versatility, temperature tolerance, and production of technologically applicable enzymes. We have biochemically characterized from the Ba type strain (CBS 8244) the GH13-family maltase Ba AG2 with efficient transglycosylation activity on maltose. In the current study, transglycosylation of sucrose was studied in detail. The chemical entities of sucrose-derived oligosaccharides were determined using nuclear magnetic resonance. Several potentially prebiotic oligosaccharides with α-1,1, α-1,3, α-1,4, and α-1,6 linkages were disclosed among the products. Trisaccharides isomelezitose, erlose, and theanderose, and disaccharides maltulose and trehalulose were dominant transglycosylation products. To date no structure for yeast maltase has been determined. Structures of the Ba AG2 with acarbose and glucose in the active center were solved at 2.12 and 2.13 Å resolution, respectively. Ba AG2 exhibited a catalytic domain with a (β/α) 8 -barrel fold and Asp216, Glu274, and Asp348 as the catalytic triad. The fairly wide active site cleft contained water channels mediating substrate hydrolysis. Next to the substrate-binding pocket an enlarged space for potential binding of transglycosylation acceptors was identified. The involvement of a Glu (Glu309) at subsite +2 and an Arg (Arg233) at subsite +3 in substrate binding was shown for the first time for α-glucosidases.


    Related Citations: 
    • Structural Insight into a Yeast Maltase-The BaAG2 from Blastobotrys adeninivorans with Transglycosylating Activity
      Ernits, K., Kjeldsen, C., Persson, K., Grigor, E., Alamae, T., Visnapuu, T.
      (2021) J Fungi 7: --

    Organizational Affiliation

    Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BaAG2A, B585Blastobotrys adeninivoransMutation(s): 0 
EC: 3.2.1.20
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
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-glucopyranoseC [auth D], D [auth E], E [auth F]3N/AN/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G66431MI
GlyCosmos:  G66431MI
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MB3
Query on MB3

Download Ideal Coordinates CCD File 
F [auth A], G [auth A], I [auth B]1-methylpyrrolidin-2-one
C5 H9 N O
SECXISVLQFMRJM-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth A], J [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900007
Query on PRD_900007
C [auth D], D [auth E], E [auth F]alpha-acarboseOligosaccharide / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.03α = 90
b = 78.08β = 94.096
c = 121.93γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2016-05009
Other privateSwedenJCK-1918
Estonian Research CouncilEstoniaPUT1050

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release
  • Version 1.1: 2021-11-03
    Changes: Data collection, Database references