6KVL

Crystal structure of UDP-RebB-SrUGT76G1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural Insights into the Catalytic Mechanism of a Plant Diterpene Glycosyltransferase SrUGT76G1.

Liu, Z.Li, J.Sun, Y.Zhang, P.Wang, Y.

(2020) Plant Commun 1: 100004-100004

  • DOI: https://doi.org/10.1016/j.xplc.2019.100004
  • Primary Citation of Related Structures:  
    6KVI, 6KVJ, 6KVK, 6KVL

  • PubMed Abstract: 

    Diterpene glycosyltransferase UGT76G1 from Stevia rebaudiana (SrUGT76G1) is key to the generation of economically important steviol glycosides (SGs), a group of natural sweeteners with high-intensity sweetness. SrUGT76G1 accommodates a wide range of steviol-derived substrates and many other small molecules. We report here the crystal structures of SrUGT76G1 in complex with multiple ligands to answer how this enzyme recognizes diterpenoid aglycones and catalyzes the 1,3-sugar chain branching. A spacious pocket for sugar-acceptor binding was observed from the determined SrUGT76G1 structures, which can explain its broad substrate spectrum. Residues Gly87 and Leu204 lining the pocket play key roles in switching between diterpenoid and flavonoid glucosylation. An engineered mutant of SrUGT76G1, T284S, could catalyze a selectively increased production of next-generation sweetener rebaudioside M, with diminished side product of rebaudioside I. Taken together, these resutls provide significant insights into molecular basis of the substrate specificity of scarcely documented diterpenoid glycosyltransferases and would facilitate the structure-guided glycoengineering to produce diversified diterpenoids with new activities.


  • Organizational Affiliation

    Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-glycosyltransferase 76G1461Stevia rebaudianaMutation(s): 0 
Gene Names: UGT76G1
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AUO (Subject of Investigation/LOI)
Query on AUO

Download Ideal Coordinates CCD File 
C [auth A](8alpha,9beta,10alpha,13alpha)-13-{[beta-D-glucopyranosyl-(1->2)-[beta-D-glucopyranosyl-(1->3)]-beta-D-glucopyranosyl]oxy}kaur-16-en-18-oic acid
C38 H60 O18
DRSKVOAJKLUMCL-MMUIXFKXSA-N
UDP (Subject of Investigation/LOI)
Query on UDP

Download Ideal Coordinates CCD File 
B [auth A]URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.463α = 90
b = 97.463β = 90
c = 89.899γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina2018YFA0900600
Chinese Academy of SciencesChinaXDB27020202
Chinese Academy of SciencesChinaXDB27020103
National Natural Science Foundation of ChinaChina31700261
National Natural Science Foundation of ChinaChina31700263
National Natural Science Foundation of ChinaChina31670099
Chinese Academy of SciencesChinaZSYS-016
Chinese Academy of SciencesChina153D31KYSB20170121

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2021-01-20
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description