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- PDB-9kus: Cryo-EM structure of C-Methyltransferase from Rhododendron dauricum -

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Basic information

Entry
Database: PDB / ID: 9kus
TitleCryo-EM structure of C-Methyltransferase from Rhododendron dauricum
ComponentsC-Methyltransferase from Rhododendron dauricum
KeywordsTRANSFERASE / Methyltransferase / Dimer
Biological speciesRhododendron dauricum (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsYe, Y.M. / Dai, Z.D. / Zhang, M.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J Am Chem Soc / Year: 2025
Title: Molecular and Structural Characterization of a Chalcone di--Methyltransferase RdCMT from and Its Application in De Novo Biosynthesis of Farrerol in .
Authors: Meng Zhang / Yang-Oujie Bao / Zonglin Dai / Zhilan Qian / Haishuang Yu / Jia-Jing Zhou / Yi Chen / Zilong Wang / Kaituo Wang / Menghao Cai / Min Ye /
Abstract: Methylation plays a crucial role in drug design and optimization. While numerous methyltransferases have been characterized from plants, -methyltransferases, particularly those targeting phenolic ...Methylation plays a crucial role in drug design and optimization. While numerous methyltransferases have been characterized from plants, -methyltransferases, particularly those targeting phenolic skeletons, are rare. In this study, we identified a novel di--methyltransferase RdCMT from the medicinal plant . RdCMT catalyzes a sequential two-step 3'-/5'--methylation of naringenin chalcone, leading to the biosynthesis of farrerol. RdCMT exhibited a strict substrate specificity for chalcones. Through combinatorial catalysis, a series of -methylated flavonoids were synthesized. Moreover, farrerol was synthesized de novo in and 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 -methylated flavonoids but also offers insights into the catalytic mechanisms of -methyltransferases.
History
DepositionDec 4, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: C-Methyltransferase from Rhododendron dauricum
B: C-Methyltransferase from Rhododendron dauricum


Theoretical massNumber of molelcules
Total (without water)86,2232
Polymers86,2232
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein C-Methyltransferase from Rhododendron dauricum


Mass: 43111.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhododendron dauricum (plant)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: C-Methyltransferase from Rhododendron dauricum / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Rhododendron dauricum (plant)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of grids imaged: 1

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Processing

EM softwareName: PHENIX / Version: 1.21_5207: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60207 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0025606
ELECTRON MICROSCOPYf_angle_d0.5247590
ELECTRON MICROSCOPYf_dihedral_angle_d3.921754
ELECTRON MICROSCOPYf_chiral_restr0.042856
ELECTRON MICROSCOPYf_plane_restr0.005972

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