6LLG

Crystal Structure of Fagopyrum esculentum M UGT708C1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structures of theC-Glycosyltransferase UGT708C1 from Buckwheat Provide Insights into the Mechanism ofC-Glycosylation.

Liu, M.Wang, D.Li, Y.Li, X.Zong, G.Fei, S.Yang, X.Lin, J.Wang, X.Shen, Y.

(2020) Plant Cell 32: 2917-2931

  • DOI: 10.1105/tpc.20.00002
  • Primary Citation of Related Structures:  
    6LLG, 6LLW, 6LLZ

  • PubMed Abstract: 
  • C-Glycosyltransferases (CGTs) catalyze the formation of C-glycosidic bonds for the biosynthesis of C-glycosides, but the underlying mechanism is unclear. This process improves the solubility and bioavailability of specialized metabolites, which play ...

    C-Glycosyltransferases (CGTs) catalyze the formation of C-glycosidic bonds for the biosynthesis of C-glycosides, but the underlying mechanism is unclear. This process improves the solubility and bioavailability of specialized metabolites, which play important roles in plant growth and development and represent rich resources for drug discovery. Here, we performed functional and structural studies of the C-glycosyltransferase UGT708C1 from buckwheat (Fagopyrum esculentum). Enzymatic analysis showed that UGT708C1 is capable of utilizing both uridine-5' diphosphate galactose (UDP-galactose) and uridine-5'-diphosphate glucose (UDP-glucose) as sugar donors. Our structural studies of UGT708C1 complexed with UDP-glucose and uridine-5'-diphosphate (UDP) identified the key roles of Asp382, Gln383, Thr151, and Thr150 in recognizing the sugar moiety of the donor substrate and Phe130, Tyr102, and Phe198 in binding and stabilizing the acceptor. A systematic site-directed mutagenesis study confirmed the important roles of these residues. Further structural analysis combined with molecular dynamics simulations revealed that phloretin binds to the acceptor-binding pocket in a bent state with a precise spatial disposition and complementarity. These findings provide insights into a catalytic mechanism for C-glycosyltransferases.


    Organizational Affiliation

    Nankai University 94 Weijin Road, Nankai University, New Biology Station A208 CITY: Tianjin POSTAL_CODE: 300071 China [CN].



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UDP-glycosyltransferase 708C1AB457Fagopyrum esculentumMutation(s): 0 
Gene Names: UGT708C1CGTa
EC: 2.4.1
Find proteins for A0A0A1HA03 (Fagopyrum esculentum)
Explore A0A0A1HA03 
Go to UniProtKB:  A0A0A1HA03
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BEN
Query on BEN

Download CCD File 
B
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.745α = 90
b = 144.247β = 90
c = 69.89γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-12-23 
  • Released Date: 2020-09-09 
  • Deposition Author(s): Wang, X., Liu, M.

Funding OrganizationLocationGrant Number
National Basic Research Program of China (973 Program)China2017YFA0504801
National Basic Research Program of China (973 Program)China2018YFA0901800

Revision History 

  • Version 1.0: 2020-09-09
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references, Structure summary