9LRJ | pdb_00009lrj

Glucosyl transferase NbUGT72AY1 co-crystallized with Scopoletin and UDP2Fglucose in the presence of retinol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 
    0.312 (Depositor), 0.298 (DCC) 
  • R-Value Work: 
    0.268 (Depositor), 0.264 (DCC) 
  • R-Value Observed: 
    0.271 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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, C, D, E
A, B, C, D, E, F, G
479Nicotiana 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
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U2F (Subject of Investigation/LOI)
Query on U2F

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
L [auth C]
N [auth D]
P [auth E]
H [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E],
Q [auth F],
S [auth G]
URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE
C15 H23 F N2 O16 P2
NGTCPFGWXMBZEP-NQQHDEILSA-N
T83 (Subject of Investigation/LOI)
Query on T83

Download Ideal Coordinates CCD File 
I [auth A],
K [auth B],
M [auth C],
O [auth D],
R [auth F]
7-hydroxy-6-methoxy-2H-1-benzopyran-2-one
C10 H8 O4
RODXRVNMMDRFIK-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free:  0.312 (Depositor), 0.298 (DCC) 
  • R-Value Work:  0.268 (Depositor), 0.264 (DCC) 
  • R-Value Observed: 0.271 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.716α = 90
b = 171.782β = 93.35
c = 153.378γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata 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 Technlogy

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Database references