9LHU | pdb_00009lhu

Crystal structure of an agose isomerase mutant 5 (TsT4Ease M5) from Thermotogota bacterium with Zn


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 
    0.259 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


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Literature

Protein Engineering of Tagatose 4-Epimerase for D-Tagatose Production.

Wang, Y.Tan, Z.Wei, H.Zhang, N.Wang, L.Yang, Y.Liu, W.Zhu, L.

(2025) J Agric Food Chem 73: 12353-12363

  • DOI: https://doi.org/10.1021/acs.jafc.5c01663
  • Primary Citation of Related Structures:  
    9LHU, 9LHY

  • PubMed Abstract: 

    D-Tagatose, a promising sugar substitute with various functional properties and commercial applications, can be enzymatically converted from D-fructose by tagatose 4-epimerase. The development of an efficient tagatose 4-epimerase that catalyzes the conversion of D-fructose into D-tagatose is essential to make the production technology of D-tagatose applicable. In this study, tagatose 4-epimerase from Thermotogae ( Ts T4Ease) was engineered through semi-rational design and directed evolution, resulting in a 2.8-fold improvement in catalytic activity compared to the wild type (WT). The production of D-tagatose reached 42 g/L in 2 h. Crystal structure analysis determined the structural features with a common (α/β) 8 -TIM barrel and a Zn 2+ -binding architecture at the active center. Subsequent molecular dynamics (MD) simulations revealed that the substitutions improved substrate binding energy and stabilized the active pocket. This study offers new insights into the structure-function relationship of Ts T4Ease and provides a candidate tagatose 4-epimerase.


  • Organizational Affiliation
    • Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tagaturonate/fructuronate epimerase507Thermotogota bacteriumMutation(s): 0 
Gene Names: uxaEDHV12_03255
EC: 5.1.2.7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free:  0.259 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.784α = 90
b = 85.533β = 90
c = 108.516γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release