8WVD | pdb_00008wvd

Crystal structure of Glycosyltransferase in complex with UD1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 
    0.233 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Enzymatic Synthesis of Novel Terpenoid Glycoside Derivatives Decorated with N -Acetylglucosamine Catalyzed by UGT74AC1.

Li, J.Li, R.Shang, N.Men, Y.Cai, Y.Zeng, Y.Liu, W.Yang, J.Sun, Y.

(2024) J Agric Food Chem 72: 14255-14263

  • DOI: https://doi.org/10.1021/acs.jafc.4c02832
  • Primary Citation Related Structures: 
    8WVD

  • PubMed Abstract: 

    The addition of the O -linked N -acetylglucosamine ( O -GlcNAc) is a significant modification for active molecules, such as proteins, carbohydrates, and natural products. However, the synthesis of terpenoid glycoside derivatives decorated with GlcNAc remains a challenging task due to the absence of glycosyltransferases, key enzymes for catalyzing the transfer of GlcNAc to terpenoids. In this study, we demonstrated that the enzyme mutant UGT74AC1 T79Y/L48M/R28H/L109I/S15A/M76L/H47R efficiently transferred GlcNAc from uridine diphosphate (UDP)-GlcNAc to a variety of terpenoids. This powerful enzyme was employed to synthesize GlcNAc-decorated derivatives of terpenoids, including mogrol, steviol, andrographolide, protopanaxadiol, glycyrrhetinic acid, ursolic acid, and betulinic acid for the first time. To unravel the mechanism of UDP-GlcNAc recognition, we determined the X-ray crystal structure of the inactivated mutant UGT74AC1 His18A/Asp111A in complex with UDP-GlcNAc at a resolution of 1.66 Å. Through molecular dynamic simulation and activity analysis, we revealed the molecular mechanism and catalytically important amino acids directly involved in the recognition of UDP-GlcNAc. Overall, this study not only provided a potent biocatalyst capable of glycodiversifying natural products but also elucidated the structural basis for UDP-GlcNAc recognition by glycosyltransferases.


  • Organizational Affiliation
    • National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.

Macromolecule Content 

  • Total Structure Weight: 51.83 kDa 
  • Atom Count: 3,945 
  • Modeled Residue Count: 450 
  • Deposited Residue Count: 454 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycosyltransferase454Siraitia grosvenoriiMutation(s): 0 
Gene Names: UDPG1
EC: 2.4.1 (PDB Primary Data), 2.4.1.350 (UniProt)
UniProt
Find proteins for K7NBW3 (Siraitia grosvenorii)
Explore K7NBW3 
Go to UniProtKB:  K7NBW3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK7NBW3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UD1
(Subject of Investigation/LOI)

Query on UD1



Download:Ideal Coordinates CCD File
B [auth A]URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
C17 H27 N3 O17 P2
LFTYTUAZOPRMMI-CFRASDGPSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free:  0.233 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.867α = 90
b = 68.825β = 90
c = 142.689γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Structure summary