6JTD

Crystal structure of TcCGT1 in complex with UDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular and Structural Characterization of a Promiscuous C-Glycosyltransferase from Trollius chinensis.

He, J.B.Zhao, P.Hu, Z.M.Liu, S.Kuang, Y.Zhang, M.Li, B.Yun, C.H.Qiao, X.Ye, M.

(2019) Angew.Chem.Int.Ed.Engl. 58: 11513-11520

  • DOI: 10.1002/anie.201905505

  • PubMed Abstract: 
  • In this work, we explored the catalytic promiscuity of TcCGT1, a new C-glycosyltransferase (CGT) from the medicinal plant Trollius chinensis. TcCGT1 could efficiently and regio-specifically catalyze 8-C-glycosylation of 36 flavones and other flavonoi ...

    In this work, we explored the catalytic promiscuity of TcCGT1, a new C-glycosyltransferase (CGT) from the medicinal plant Trollius chinensis. TcCGT1 could efficiently and regio-specifically catalyze 8-C-glycosylation of 36 flavones and other flavonoids, and could also catalyze the O-glycosylation of diverse phenolics. Moreover, the crystal structure of TcCGT1 in complex with uridine diphosphate was determined at 1.85 Å resolution. Structural analysis with molecular docking revealed a new model for catalytic mechanism of TcCGT1, which was initiated by substrate spontaneous deprotonation. The spacious binding pocket explains the robust substrate promiscuity, and binding pose of the substrate determines C- or O-glycosylation activity. Site-directed mutagenesis at two residues (I94E and G284K) switched C- to O-glycosylation. This work highlights TcCGT1 as the first plant CGT with a crystal structure and the first flavone 8-C-glycosyltransferase, and provides a basis for protein engineering to design efficient glycosylation biocatalysts for drug discovery.


    Organizational Affiliation

    Peking University, CHINA.,Peking University, State Key Laboratory of Natural and Biomimetic Drugs, 38 Xueyuan Road, 100191, Beijing, CHINA.,Peking University, School of Pharmaceutical Sciences, 38 Xueyuan Road, 100191, Beijing, CHINA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-glycosyltransferase
A, B
483N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
UDP
Query on UDP

Download SDF File 
Download CCD File 
A, B
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.304α = 90.00
b = 108.702β = 106.17
c = 90.432γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-04-10 
  • Released Date: 2019-06-19 
  • Deposition Author(s): Zhao, P., Yun, C.H.

Revision History 

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-07-24
    Type: Data collection, Database references
  • Version 1.2: 2019-08-14
    Type: Data collection, Database references