9DGC | pdb_00009dgc

Tetrahydroprotoberberine N-methyltransferase E207A mutant in complex with (S)-reticuline and SAM

PDB DOI: https://doi.org/10.2210/pdb9DGC/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.208 (Depositor), 0.210 (DCC)
R-Value Work:
0.175 (Depositor), 0.177 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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.

Macromolecule Content

Total Structure Weight: 44.47 kDa
Atom Count: 2,999
Modeled Residue Count: 339
Deposited Residue Count: 383
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetrahydroprotoberberine N-methyltransferase	A	383	Glaucium flavum	Mutation(s): 1 EC: 2.1.1.122
UniProt
Find proteins for A0A5S8WF76 (Glaucium flavum) Explore A0A5S8WF76 Go to UniProtKB: A0A5S8WF76
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5S8WF76
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM (Subject of Investigation/LOI) Query on SAM Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
REN (Subject of Investigation/LOI) Query on REN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(S)-reticuline C₁₉ H₂₃ N O₄ BHLYRWXGMIUIHG-HNNXBMFYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.208 (Depositor), 0.210 (DCC)
R-Value Work: 0.175 (Depositor), 0.177 (DCC)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.989	α = 90
b = 103.989	β = 90
c = 82.444	γ = 120

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-17

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.