6LYI

Crystal structure of a N-methyltransferase CkTbS from Camellia assamica var. kucha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Identification and characterization of N9-methyltransferase involved in converting caffeine into non-stimulatory theacrine in tea.

Zhang, Y.H.Li, Y.F.Wang, Y.Tan, L.Cao, Z.Q.Xie, C.Xie, G.Gong, H.B.Sun, W.Y.Ouyang, S.H.Duan, W.J.Lu, X.Ding, K.Kurihara, H.Hu, D.Zhang, Z.M.Abe, I.He, R.R.

(2020) Nat Commun 11: 1473-1473

  • DOI: https://doi.org/10.1038/s41467-020-15324-7
  • Primary Citation of Related Structures:  
    6LYH, 6LYI

  • PubMed Abstract: 

    Caffeine is a major component of xanthine alkaloids and commonly consumed in many popular beverages. Due to its occasional side effects, reduction of caffeine in a natural way is of great importance and economic significance. Recent studies reveal that caffeine can be converted into non-stimulatory theacrine in the rare tea plant Camellia assamica var. kucha (Kucha), which involves oxidation at the C8 and methylation at the N9 positions of caffeine. However, the underlying molecular mechanism remains unclear. Here, we identify the theacrine synthase CkTcS from Kucha, which possesses novel N9-methyltransferase activity using 1,3,7-trimethyluric acid but not caffeine as a substrate, confirming that C8 oxidation takes place prior to N9-methylation. The crystal structure of the CkTcS complex reveals the key residues that are required for the N9-methylation, providing insights into how caffeine N-methyltransferases in tea plants have evolved to catalyze regioselective N-methylation through fine tuning of their active sites. These results may guide the future development of decaffeinated drinks.


  • Organizational Affiliation

    International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-methyltransferase CkTbS
A, B
371Camellia sinensis var. assamicaMutation(s): 0 
UniProt
Find proteins for Q9FZN8 (Camellia sinensis)
Explore Q9FZN8 
Go to UniProtKB:  Q9FZN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FZN8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.768α = 90
b = 144.768β = 90
c = 76.18γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-04-01
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description