7WH9

holo structure of emodin 1-OH O-methyltransferase complex with emodin and S-Adenosyl-L-homocysteine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Characterization and Structural Analysis of Emodin- O -Methyltransferase from Aspergillus terreus.

Xue, Y.Liang, Y.Zhang, W.Geng, C.Feng, D.Huang, X.Dong, S.Zhang, Y.Sun, J.Qi, F.Lu, X.

(2022) J Agric Food Chem 70: 5728-5737

  • DOI: https://doi.org/10.1021/acs.jafc.2c01281
  • Primary Citation of Related Structures:  
    7WH9

  • PubMed Abstract: 

    All O -methylated derivatives of emodin, including physcion, questin, and 1- O -methylemodin, show potential antifungal activities. Notably, emodin and questin are two pivotal intermediates of geodin biosynthesis in Aspergillus terreus . Although most of the geodin biosynthetic steps have been investigated, the key O -methyltransferase (OMT) responsible for the O -methylation of emodin to generate questin has remained unidentified. Herein, through phylogenetic tree analysis and in vitro biochemical assays, the long-sought class II emodin- O -methyltransferase GedA has been functionally characterized. Additionally, the catalytic mechanism and key residues at the catalytic site of GedA were elucidated by enzyme-substrate-methyl donor analogue ternary complex crystal structure determination and site-directed mutagenesis. As we demonstrate, GedA adopts a typical general acid/base (E446/H373)-mediated transmethylation mechanism. In particular, residue D374 is also crucial for efficient catalysis through blocking the formation of intramolecular hydrogen bonds in emodin. This study will facilitate future engineering of GedA for the production of physcion or other site-specific O -methylated anthraquinone derivatives with potential applications as biopesticides.


  • Organizational Affiliation

    Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
O-methyltransferase gedA
A, B, C
506Aspergillus terreusMutation(s): 0 
Gene Names: gedAATEG_08449
EC: 2.1.1.283
UniProt
Find proteins for Q0CCY5 (Aspergillus terreus (strain NIH 2624 / FGSC A1156))
Explore Q0CCY5 
Go to UniProtKB:  Q0CCY5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0CCY5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162.093α = 90
b = 162.093β = 90
c = 130.219γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
xia2data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
xia2data reduction
PHASERphasing
AutoSolphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31972855
Ministry of Science and Technology (MoST, China)China2021YFC2102600

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-11
    Type: Initial release
  • Version 1.1: 2023-01-18
    Changes: Database references
  • Version 1.2: 2024-05-29
    Changes: Data collection