6L5S

crystal structure of GgCGT in complex with UDP-Glu


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

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


Literature

Functional Characterization and Structural Basis of an Efficient Di-C-glycosyltransferase fromGlycyrrhiza glabra.

Zhang, M.Li, F.D.Li, K.Wang, Z.L.Wang, Y.X.He, J.B.Su, H.F.Zhang, Z.Y.Chi, C.B.Shi, X.M.Yun, C.H.Zhang, Z.Y.Liu, Z.M.Zhang, L.R.Yang, D.H.Ma, M.Qiao, X.Ye, M.

(2020) J Am Chem Soc 142: 3506-3512

  • DOI: https://doi.org/10.1021/jacs.9b12211
  • Primary Citation of Related Structures:  
    6L5P, 6L5Q, 6L5R, 6L5S, 6L7H

  • PubMed Abstract: 

    A highly efficient di- C -glycosyltransferase GgCGT was discovered from the medicinal plant Glycyrrhiza glabra . GgCGT catalyzes a two-step di- C -glycosylation of flopropione-containing substrates with conversion rates of >98%. To elucidate the catalytic mechanisms of GgCGT, we solved its crystal structures in complex with UDP-Glc, UDP-Gal, UDP/phloretin, and UDP/nothofagin, respectively. Structural analysis revealed that the sugar donor selectivity was controlled by the hydrogen-bond interactions of sugar hydroxyl groups with D390 and other key residues. The di- C -glycosylation capability of GgCGT was attributed to a spacious substrate-binding tunnel, and the G389K mutation could switch di- to mono- C -glycosylation. GgCGT is the first di- C -glycosyltransferase with a crystal structure, and the first C -glycosyltransferase with a complex structure containing a sugar acceptor. This work could benefit the development of efficient biocatalysts to synthesize C -glycosides with medicinal potential.


  • Organizational Affiliation

    State Key Laboratory of Natural and Biomimetic Drugs, 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
MoleculeChains Sequence LengthOrganismDetailsImage
GgCGT474Glycyrrhiza glabraMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.376α = 90
b = 70.62β = 90
c = 108.402γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-03-04
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description