9J9K | pdb_00009j9k

Glucosyl transferase NbUGT72AY1 co-crystallized with Scopoletin and UDP2F glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 
    0.258 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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Literature

beta-Carotene alleviates substrate inhibition caused by asymmetric cooperativity.

Liao, J.Shahul Hameed, U.F.Hoffmann, T.D.Kurze, E.Sun, G.Steinchen, W.Nicoli, A.Di Pizio, A.Kuttler, C.Song, C.Catici, D.A.M.Assaad-Gerbert, F.Hoffmann, T.Arold, S.T.Schwab, W.G.

(2025) Nat Commun 16: 3065-3065

  • DOI: https://doi.org/10.1038/s41467-025-58259-7
  • Primary Citation of Related Structures:  
    8J2U, 8J2V, 8J2Z, 8J31, 9J9K, 9LRJ

  • PubMed Abstract: 

    Enzymes are essential catalysts in biological systems. Substrate inhibition, once dismissed, is now observed in 20% of enzymes 1 and is attributed to the formation of an unproductive enzyme-substrate complex, with no structural evidence of unproductivity provided to date 1-6 . This study uncovers the molecular mechanism of substrate inhibition in tobacco glucosyltransferase NbUGT72AY1, which transfers glucose to phenols for plant protection. The peculiarity that β-carotene strongly attenuates the substrate inhibition of NbUGT72AY1, despite being a competitive inhibitor, allows to determine the conformational changes that occur during substrate binding in both active and substrate-inhibited complexes. Crystallography reveals structurally different ternary enzyme-substrate complexes that do not conform to classical mechanisms. An alternative pathway suggests substrates bind randomly, but the reaction occurs only if a specific order is followed (asymmetric cooperativity). This unreported paradigm explains substrate inhibition and reactivation by competitive inhibitors, opening new research avenues in metabolic regulation and industrial applications.


  • Organizational Affiliation

    Biotechnology of Natural Products, School of Life Sciences, Technical University of Munich, 85354, Freising, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycosyltransferase
A, B
475Nicotiana benthamianaMutation(s): 0 
EC: 2.4.1
UniProt
Find proteins for A0A8K1ZRH3 (Nicotiana benthamiana)
Explore A0A8K1ZRH3 
Go to UniProtKB:  A0A8K1ZRH3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8K1ZRH3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.607α = 90
b = 114.919β = 103.12
c = 104.249γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateSaudi ArabiaKing Abdullah University of Science and Technology

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Database references, Structure summary