9ISA | pdb_00009isa

Dimeric amylosucrase from Deinococcus geothermalis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 
    0.220 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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Literature

Construction and enzymatic characterization of a monomeric variant of dimeric amylosucrase from Deinococcus geothermalis.

Oh, J.S.Kim, D.S.So, Y.S.Hong, S.Yoo, S.H.Park, C.S.Park, J.H.Seo, D.H.

(2025) Int J Biol Macromol 285: 138249-138249

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.138249
  • Primary Citation of Related Structures:  
    9ISA

  • PubMed Abstract: 

    Amylosucrase (ASase; E.C. 2.4.1.4), a member of glycoside hydrolase family 13 (GH13), produces α-1,4-glucans and sucrose isomers using sucrose as its sole substrate. This study identifies and characterizes the dimeric structure of ASase from Deinococcus geothermalis (DgAS), highlighting essential amino acid residues for maintaining the dimeric state. The monomeric form, DgAS R30A, exhibited a higher affinity for sucrose compared to the wild-type (WT), especially during the formation of the ASase-glucose intermediate complex and subsequent hydrolysis. Notably, DgAS R30A produced a higher proportion of α-glucans with a degree of polymerization (DP) of ≤20 and fewer α-glucans with a DP of ≥31. This suggested that the reduced surface area of the oligosaccharide binding site in the monomeric form led to decreased binding of longer-chain maltooligosaccharides, favoring the formation of shorter DP α-glucans. Kinetic analysis revealed significantly lower Michaelis constants (K m ) for DgAS R30A's total and hydrolysis activities, with the overall performance (k cat /K m ) values for DgAS R30A exceeded those of the WT at all sucrose concentrations. Here, we report the first high-resolution homodimeric DgAS structure, revealing conserved active site residues and a unique dimerization interface. This study enhances our understanding of the molecular factors influencing the oligomeric state and enzyme activities.


  • Organizational Affiliation
    • Department of Food Science and Biotechnology, and Carbohydrate Bioproduct Research Center, Sejong University, Seoul 05006, Republic of Korea.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amylosucrase
A, B
645Deinococcus geothermalis DSM 11300Mutation(s): 0 
Gene Names: Dgeo_0572
UniProt
Find proteins for Q1J0W0 (Deinococcus geothermalis (strain DSM 11300 / CIP 105573 / AG-3a))
Explore Q1J0W0 
Go to UniProtKB:  Q1J0W0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1J0W0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free:  0.220 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.917α = 90
b = 149.917β = 90
c = 188.131γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2021R1C1C1004489

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release