6LYH

Crystal structure of tea N9-methyltransferase CkTcS in complex with SAH and 1,3,7-trimethyluric acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.264 

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Ligand Structure Quality Assessment 


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 CkTcS363Camellia 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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
I [auth B]
K [auth A]
M [auth C]
O [auth D]
Q [auth E]
I [auth B],
K [auth A],
M [auth C],
O [auth D],
Q [auth E],
S [auth F],
U [auth G],
W [auth H]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
EXU
Query on EXU

Download Ideal Coordinates CCD File 
J [auth B]
L [auth A]
N [auth C]
P [auth D]
R [auth E]
J [auth B],
L [auth A],
N [auth C],
P [auth D],
R [auth E],
T [auth F],
V [auth G],
X [auth H]
1,3,7-trimethyl-9H-purine-2,6,8-trione
C8 H10 N4 O3
BYXCFUMGEBZDDI-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.264 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.744α = 90.211
b = 86.812β = 90.039
c = 123.258γ = 90.172
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing
Cootmodel building
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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