8ITA | pdb_00008ita

A reversible glycosyltransferase of tectorigenin - Bc7OUGT complexed with UDP and tectorigenin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.272 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.218 (Depositor) 
  • R-Value Observed: 
    0.221 (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 1.1 of the entry. See complete history

Literature

Functional characterization and structural basis of a reversible glycosyltransferase involves in plant chemical defence.

Cheng, W.Fang, X.Guan, Z.Yao, Y.Xu, Z.Bi, Y.Ren, K.Li, J.Chen, F.Chen, X.Ma, W.Chu, Z.Deng, Z.Zhang, Z.Lu, L.

(2023) Plant Biotechnol J 21: 2611-2624

  • DOI: https://doi.org/10.1111/pbi.14157
  • Primary Citation Related Structures: 
    8INP, 8ITA

  • PubMed Abstract: 

    Plants experience numerous biotic stresses throughout their lifespan, such as pathogens and pests, which can substantially affect crop production. In response, plants have evolved various metabolites that help them withstand these stresses. Here, we show that two specialized metabolites in the herbaceous perennial Belamcanda chinensis, tectorigenin and its glycoside tectoridin, have diverse defensive effects against phytopathogenic microorganisms and antifeeding effects against insect pest. We further functionally characterized a 7-O-uridine diphosphate glycosyltransferase Bc7OUGT, which catalyses a novel reversible glycosylation of tectorigenin and tectoridin. To elucidate the catalytic mechanisms of Bc7OUGT, we solved its crystal structure in complex with UDP and UDP/tectorigenin respectively. Structural analysis revealed the Bc7OUGT possesses a narrow but novel substrate-binding pocket made up by plentiful aromatic residues. Further structure-guided mutagenesis of these residues increased both glycosylation and deglycosylation activities. The catalytic reversibility of Bc7OUGT was also successfully applied in an one-pot aglycon exchange reaction. Our findings demonstrated the promising biopesticide activity of tectorigenin and its glycosides, and the characterization and mechanistic study of Bc7OUGT could facilitate the design of novel reversible UGTs to produce valuable glycosides with health benefits for both plants and humans.


  • Organizational Affiliation
    • Department of Integrated Traditional Chinese Medicine and Western Medicine, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.

Macromolecule Content 

  • Total Structure Weight: 52.4 kDa 
  • Atom Count: 3,427 
  • Modeled Residue Count: 429 
  • Deposited Residue Count: 467 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bc7OUGT467Iris domesticaMutation(s): 0 
EC: 2.4.1
UniProt
Find proteins for A0AA96QCN7 (Iris domestica)
Explore A0AA96QCN7 
Go to UniProtKB:  A0AA96QCN7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AA96QCN7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 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
R0U
(Subject of Investigation/LOI)

Query on R0U



Download:Ideal Coordinates CCD File
B [auth A]3-(4-hydroxyphenyl)-6-methoxy-5,7-bis(oxidanyl)chromen-4-one
C16 H12 O6
OBBCRPUNCUPUOS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.272 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.218 (Depositor) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.238α = 90
b = 83.474β = 90
c = 158.763γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
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)China32100413

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-23
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Database references