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 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    6JTD

  • PubMed Abstract: 
  • Herein, the catalytic promiscuity of TcCGT1, a new C-glycosyltransferase (CGT) from the medicinal plant Trollius chinensis is explored. TcCGT1 could efficiently and regio-specifically catalyze the 8-C-glycosylation of 36 flavones and other flavonoids and could also catalyze the O-glycosylation of diverse phenolics ...

    Herein, the catalytic promiscuity of TcCGT1, a new C-glycosyltransferase (CGT) from the medicinal plant Trollius chinensis is explored. TcCGT1 could efficiently and regio-specifically catalyze the 8-C-glycosylation of 36 flavones and other flavonoids and could also catalyze the O-glycosylation of diverse phenolics. The crystal structure of TcCGT1 in complex with uridine diphosphate was determined at 1.85 Å resolution. Molecular docking revealed a new model for the catalytic mechanism of TcCGT1, which is initiated by the spontaneous deprotonation of the substrate. The spacious binding pocket explains the substrate promiscuity, and the 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. TcCGT1 is the first plant CGT with a crystal structure and the first flavone 8-C-glycosyltransferase described. This provides a basis for designing efficient glycosylation biocatalysts.


    Organizational Affiliation

    State Key Laboratory of Natural and Biomimetic Drugs & Key Laboratory of Molecular Cardiovascular Sciences of Ministry of Education, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
C-glycosyltransferaseA, B483Trollius chinensisMutation(s): 0 
Gene Names: CGT1
EC: 2.4.1
UniProt
Find proteins for A0A4Y5RXX8 (Trollius chinensis)
Explore A0A4Y5RXX8 
Go to UniProtKB:  A0A4Y5RXX8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4Y5RXX8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UDP
Query on UDP

Download Ideal Coordinates CCD File 
BA [auth B],
C [auth A]
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth A],
AB [auth B],
BB [auth B],
CA [auth B],
CB [auth B],
AA [auth A],
AB [auth B],
BB [auth B],
CA [auth B],
CB [auth B],
D [auth A],
DA [auth B],
DB [auth B],
E [auth A],
EA [auth B],
EB [auth B],
F [auth A],
FA [auth B],
FB [auth B],
G [auth A],
GA [auth B],
GB [auth B],
H [auth A],
HA [auth B],
HB [auth B],
I [auth A],
IA [auth B],
IB [auth B],
J [auth A],
JA [auth B],
JB [auth B],
K [auth A],
KA [auth B],
KB [auth B],
L [auth A],
LA [auth B],
LB [auth B],
M [auth A],
MA [auth B],
N [auth A],
NA [auth B],
O [auth A],
OA [auth B],
P [auth A],
PA [auth B],
Q [auth A],
QA [auth B],
R [auth A],
RA [auth B],
S [auth A],
SA [auth B],
T [auth A],
TA [auth B],
U [auth A],
UA [auth B],
V [auth A],
VA [auth B],
W [auth A],
WA [auth B],
X [auth A],
XA [auth B],
Y [auth A],
YA [auth B],
Z [auth A],
ZA [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-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 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.304α = 90
b = 108.702β = 106.17
c = 90.432γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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