8ZI7 | pdb_00008zi7

Crystal structure of SrUGT76G4 in complex with Rubusoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.232 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Characterization of Sr UGT76G4 reveals a key residue for regioselectivity and efficient Reb M synthesis.

Wang, Y.Li, T.Zheng, Y.Guo, C.Li, K.Jia, X.Zhu, L.Chen, K.Yin, H.

(2025) Proc Natl Acad Sci U S A 122: e2504698122-e2504698122

  • DOI: https://doi.org/10.1073/pnas.2504698122
  • Primary Citation Related Structures: 
    8ZI6, 8ZI7

  • PubMed Abstract: 

    Steviol glycosides (SGs) from Stevia rebaudiana are prized as noncaloric sweeteners, with rebaudioside M (Reb M)-a next-generation SG known for its sucrose-like sweetness and lack of off-tastes-standing out for its superior sensory profile. However, Reb M's limited natural abundance impedes its commercial production. Here, we report the identification of a glucosyltransferase, UGT76G4 that efficiently catalyzes the conversion of Reb D to Reb M with a strong preference for C19 glycosylation. Structural and functional analyses, including X-ray crystallography, molecular dynamics simulations, and mutagenesis, revealed key residues in UGT76G4 that dictate its regioselectivity, with residue 200 playing a pivotal role. Engineered UGT76G4 variants, including Q199I/G200Y and H155S/Q199I/G200Y, enhanced Reb E and Reb D conversion efficiency by 1.46-fold and 23-fold, respectively, compared to UGT76G1. The engineered variants offer a promising pathway for increasing Reb M production, advancing biotechnological strategies for steviol glycoside biosynthesis and optimizing plant metabolic engineering approaches. Our findings deepen the understanding of SG biosynthesis and provide a basis for sustainable production of high-value sweeteners.


  • Organizational Affiliation
    • Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Dalian Technology Innovation Center for Green Agriculture, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People's Republic of China.

Macromolecule Content 

  • Total Structure Weight: 53.16 kDa 
  • Atom Count: 3,412 
  • Modeled Residue Count: 403 
  • Deposited Residue Count: 458 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
UGT-glycosyltransferase 76G4458Stevia rebaudianaMutation(s): 0 
EC: 2.4.1
UniProt
Find proteins for Q6VAB4 (Stevia rebaudiana)
Explore Q6VAB4 
Go to UniProtKB:  Q6VAB4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6VAB4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AQ9
(Subject of Investigation/LOI)

Query on AQ9



Download:Ideal Coordinates CCD File
C [auth A]1-O-[(8alpha,9beta,10alpha,13alpha)-13-(beta-D-glucopyranosyloxy)-18-oxokaur-16-en-18-yl]-beta-D-glucopyranose
C32 H50 O13
YWPVROCHNBYFTP-OSHKXICASA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
G [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA

Query on IPA



Download:Ideal Coordinates CCD File
F [auth A]ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
SCN

Query on SCN



Download:Ideal Coordinates CCD File
D [auth A],
H [auth A]
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
EOH

Query on EOH



Download:Ideal Coordinates CCD File
E [auth A],
I [auth A]
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
B [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.232 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.026α = 90
b = 77.228β = 90
c = 86.134γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
autoPROCdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release
  • Version 1.1: 2025-12-03
    Changes: Database references