8XGX | pdb_00008xgx

beta-1,4-galacosyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 
    0.253 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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Literature

Crystal structure and structure-guided tunnel engineering in a bacterial beta-1,4-galactosyltransferase.

Luo, G.Huang, Z.Zhu, Y.Chen, J.Hou, X.Ni, D.Xu, W.Zhang, W.Rao, Y.Mu, W.

(2024) Int J Biol Macromol 279: 135374-135374

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.135374
  • Primary Citation of Related Structures:  
    8XC8, 8XGX, 8XKD, 8XLZ, 8XOC

  • PubMed Abstract: 

    Lacto-N-neotetraose (LNnT), a representative oligosaccharide found in human milk, has been previously examined for its beneficial traits. However, the LNnT titer is limited by the efficient glycosyltransferase pathway, particularly with respect to the catalysis of rate-limiting steps. As data on the crystal structure of the key enzyme required for synthesizing LNnT are lacking, the synthesis of LNnT remains an uncertainty. Here, for the first time we report the three-dimensional structure of a bacterial β-1,4-galactosyltransferase, Aaβ4GalT, and analyze the critical role played by residues in its catalytic efficacy. Guided by structural insights, we engineered this enzyme to enhance its catalytic efficiency using structure-guided tunnel engineering. The mutant enzyme L5 (K155M/H156D/F157W/K185M/Q216V) so produced, showed a 50-fold enhancement in catalytic activity. Crystal structure analysis revealed that the mechanism underlying the improvement in activity was of the swing door type. The closed conformation formed by dense hydrophobic packing with Q216V-K155M widened and permitted substrate entry. Our results show that altering the tunnel conformation helped appropriately accommodate the substrate for catalysis and provide a structural basis for the modification of other glycosyltransferases.


  • Organizational Affiliation
    • State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycosyltransferase family 25 protein
A, B
251Aggregatibacter actinomycetemcomitans NUM4039Mutation(s): 0 
Gene Names: FXB68_02155
UniProt
Find proteins for A0A5D0ENI3 (Aggregatibacter actinomycetemcomitans)
Explore A0A5D0ENI3 
Go to UniProtKB:  A0A5D0ENI3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5D0ENI3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free:  0.253 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.84α = 90
b = 87.84β = 90
c = 140.24γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China2022YFC2104900
National Natural Science Foundation of China (NSFC)China32302010
Other privateBK20231043

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release