9DG8 | pdb_00009dg8

Tetrahydroprotoberberine N-methyltransferase E204A mutant in complex with (S)-reticuline and SAM

• PDB DOI: https://doi.org/10.2210/pdb9DG8/pdb

• Classification: TRANSFERASE
• Organism(s): Glaucium flavum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-09-02 Released: 2025-09-17 
• Deposition Author(s): Lang, D.E., Ng, K.K.S.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.166 (DCC) 

Starting Model: experimental

Literature

The stereospecific activities of the tetrahydroprotoberberine N-methyltransferase with alternative substrates provide insight into the catalytic mechanisms of benzylisoquinoline alkaloid N-methylation.

Lang, D.E., Ng, K.K.S., Rehman, F., Morris, J.S., Facchini, P.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 44.43 kDa 
• Atom Count: 3,024 
• Modeled Residue Count: 335 
• Deposited Residue Count: 382 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetrahydroprotoberberine N-methyltransferase	A	382	Glaucium flavum	Mutation(s): 1  EC: 2.1.1.122
UniProt
Find proteins for A0A5S8WF76 (Glaucium flavum) Explore A0A5S8WF76  Go to UniProtKB:  A0A5S8WF76

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM (Subject of Investigation/LOI)	B [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
REN (Subject of Investigation/LOI)	C [auth A]	(S)-reticuline C19 H23 N O4 BHLYRWXGMIUIHG-HNNXBMFYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.166 (DCC) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.098	α = 90
b = 104.098	β = 90
c = 82.196	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-17 
Deposition Author(s): Lang, D.E., Ng, K.K.S.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History  

• Version 1.0: 2025-09-17
  Type: Initial release