8XFW | pdb_00008xfw

Crystal structure of MiCGT(M148A/V190T/S121D) in complex with UDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.239 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

An efficient C-glycoside production platform enabled by rationally tuning the chemoselectivity of glycosyltransferases.

Li, M.Zhou, Y.Wen, Z.Ni, Q.Zhou, Z.Liu, Y.Zhou, Q.Jia, Z.Guo, B.Ma, Y.Chen, B.Zhang, Z.M.Wang, J.B.

(2024) Nat Commun 15: 8893-8893

  • DOI: https://doi.org/10.1038/s41467-024-53209-1
  • Primary Citation Related Structures: 
    8XFH, 8XFW

  • PubMed Abstract: 

    Despite the broad potential applications of C-glycosides, facile synthetic methods remain scarce. Transforming glycosyltransferases with promiscuous or natural O-specific chemoselectivity to C-glycosyltransferases is challenging. Here, we employ rational directed evolution of the glycosyltransferase MiCGT to generate MiCGT-QDP and MiCGT-ATD mutants which either enhance C-glycosylation or switch to O-glycosylation, respectively. Structural analysis and computational simulations reveal that substrate binding mode govern C-/O-glycosylation selectivity. Notably, directed evolution and mechanism analysis pinpoint the crucial residues dictating the binding mode, enabling the rational design of four enzymes with superior non-inherent chemoselectivity, despite limited sequence homology. Moreover, our best mutants undergo testing with 34 substrates, demonstrating superb chemoselectivities, regioselectivities, and activities. Remarkably, three C-glycosides and an O-glycoside are produced on a gram scale, demonstrating practical utility. This work establishes a highly selective platform for diverse glycosides, and offers a practical strategy for creating various types of glycosylation platforms to access pharmaceutically and medicinally interesting products.


  • Organizational Affiliation
    • Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education) and Key Laboratory of Phytochemical R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081, Changsha, P. R. China.

Macromolecule Content 

  • Total Structure Weight: 102.31 kDa 
  • Atom Count: 6,683 
  • Modeled Residue Count: 888 
  • Deposited Residue Count: 918 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
UDP-glycosyltransferase 13
A, B
459Mangifera indicaMutation(s): 3 
Gene Names: CGT
EC: 2.4.1
UniProt
Find proteins for A0A0M4KE44 (Mangifera indica)
Explore A0A0M4KE44 
Go to UniProtKB:  A0A0M4KE44
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M4KE44
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on UDP



Download:Ideal Coordinates CCD File
C [auth A]URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.239 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.194α = 90
b = 103.617β = 90
c = 110.195γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data reduction
PHASESphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-18
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Database references
  • Version 1.2: 2025-07-09
    Changes: Database references