9J9K | pdb_00009j9k

Glucosyl transferase NbUGT72AY1 co-crystallized with Scopoletin and UDP2F glucose

• PDB DOI: https://doi.org/10.2210/pdb9J9K/pdb
• Entry: 9J9K supersedes: 8J2T

• Classification: TRANSFERASE
• Organism(s): Nicotiana benthamiana
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-08-22 Released: 2024-09-04 
• Deposition Author(s): Arold, S.T., Hameed, U.F.S.
• Funding Organization(s): Other private

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Experimental Data Snapshot

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

Starting Model: experimental

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

• PubMed: 40157902 
• DOI: https://doi.org/10.1038/s41467-025-58259-7
• Primary Citation 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.

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Organizational Affiliation: 
• Biotechnology of Natural Products, School of Life Sciences, Technical University of Munich, 85354, Freising, Germany.
KAUST Center of Excellence for Smart Health, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, 35043, Marburg, Germany.
Department of Chemistry, Philipps-University Marburg, 35043, Marburg, Germany.
Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354, Freising, Germany.
Chemoinformatics and Protein Modelling, School of Life Sciences, Technical University of Munich, 85354, Freising, Germany.
Analysis and Mathematical Biology, Technical University of Munich, School of Computation, Information and Technology, 85748, Garching, Germany.
State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, 230036, Hefei, Anhui, China.
Center for Protein Assemblies (CPA), Technical University of Munich, 85748, Garching, Germany.
Biotechnology of Natural Products, School of Life Sciences, Technical University of Munich, 85354, Freising, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 108.1 kDa 
• Atom Count: 7,493 
• Modeled Residue Count: 938 
• Deposited Residue Count: 950 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A, B	475	Nicotiana benthamiana	Mutation(s): 0  EC: 2.4.1
UniProt
Find proteins for A0A8K1ZRH3 (Nicotiana benthamiana) Explore A0A8K1ZRH3  Go to UniProtKB:  A0A8K1ZRH3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U2F (Subject of Investigation/LOI)	D [auth A], F [auth B]	URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE C15 H23 F N2 O16 P2 NGTCPFGWXMBZEP-NQQHDEILSA-N
T83 (Subject of Investigation/LOI)	C [auth A], E [auth B]	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: 3.15 Å
• R-Value Free:  0.258 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.190 (Depositor) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.607	α = 90
b = 114.919	β = 103.12
c = 104.249	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Arold, S.T., Hameed, U.F.S.
• This entry supersedes: 8J2T

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Funding Organization	Location	Grant Number
Other private	Saudi Arabia	King Abdullah University of Science and Technology

Revision History  

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