9KUS | pdb_00009kus

Cryo-EM structure of C-Methyltransferase from Rhododendron dauricum


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular and Structural Characterization of a Chalcone di- C -Methyltransferase RdCMT from Rhododendron dauricum and Its Application in De Novo Biosynthesis of Farrerol in Pichia pastoris .

Zhang, M.Bao, Y.O.Dai, Z.Qian, Z.Yu, H.Zhou, J.J.Chen, Y.Wang, Z.Wang, K.Cai, M.Ye, M.

(2025) J Am Chem Soc 147: 17132-17143

  • DOI: https://doi.org/10.1021/jacs.5c02654
  • Primary Citation of Related Structures:  
    9KUS

  • PubMed Abstract: 

    Methylation plays a crucial role in drug design and optimization. While numerous methyltransferases have been characterized from plants, C -methyltransferases, particularly those targeting phenolic skeletons, are rare. In this study, we identified a novel di- C -methyltransferase RdCMT from the medicinal plant Rhododendron dauricum . RdCMT catalyzes a sequential two-step 3'- C /5'- C -methylation of naringenin chalcone, leading to the biosynthesis of farrerol. RdCMT exhibited a strict substrate specificity for chalcones. Through combinatorial catalysis, a series of C -methylated flavonoids were synthesized. Moreover, farrerol was synthesized de novo in Nicotiana benthamiana and Pichia pastoris with yields of 0.4 mg/g (dry weight) and 149.0 mg/L, respectively. The structure of RdCMT was determined using cryo-electron microscopy (cryo-EM), revealing that residues R328 and G296 significantly influence the substrate specificity of RdCMT. This work not only introduces a potent biocatalyst for the preparation of C -methylated flavonoids but also offers insights into the catalytic mechanisms of C -methyltransferases.


  • Organizational Affiliation
    • State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-Methyltransferase from Rhododendron dauricum
A, B
391Rhododendron dauricumMutation(s): 0 
UniProt
Find proteins for A0A834H415 (Rhododendron simsii)
Explore A0A834H415 
Go to UniProtKB:  A0A834H415
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A834H415
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207:

Structure Validation

View Full Validation Report



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: 2025-05-21
    Type: Initial release
  • Version 1.1: 2025-06-04
    Changes: Data collection, Database references