Tetrahydroprotoberberine N-methyltransferase in complex with S-adenosylmethionine

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Structure-function studies of tetrahydroprotoberberineN-methyltransferase reveal the molecular basis of stereoselective substrate recognition.

Lang, D.E.Morris, J.S.Rowley, M.Torres, M.A.Maksimovich, V.A.Facchini, P.J.Ng, K.K.S.

(2019) J Biol Chem 294: 14482-14498

  • DOI: https://doi.org/10.1074/jbc.RA119.009214
  • Primary Citation of Related Structures:  
    6P3M, 6P3N, 6P3O

  • PubMed Abstract: 

    Benzylisoquinoline alkaloids (BIAs) are a structurally diverse class of plant-specialized metabolites that have been particularly well-studied in the order Ranunculales. The N -methyltransferases (NMTs) in BIA biosynthesis can be divided into three groups according to substrate specificity and amino acid sequence. Here, we report the first crystal structures of enzyme complexes from the tetrahydroprotoberberine NMT (TNMT) subclass, specifically for Gf TNMT from the yellow horned poppy ( Glaucium flavum ). Gf TNMT was co-crystallized with the cofactor S -adenosyl-l-methionine ( d min = 1.6 Å), the product S -adenosyl-l-homocysteine ( d min = 1.8 Å), or in complex with S -adenosyl-l-homocysteine and ( S )- cis-N -methylstylopine (d min = 1.8 Å). These structures reveal for the first time how a mostly hydrophobic L-shaped substrate recognition pocket selects for the ( S )- cis configuration of the two central six-membered rings in protoberberine BIA compounds. Mutagenesis studies confirm and functionally define the roles of several highly-conserved residues within and near the Gf TNMT-active site. The substrate specificity of TNMT enzymes appears to arise from the arrangement of subgroup-specific stereospecific recognition elements relative to catalytic elements that are more widely-conserved among all BIA NMTs. The binding mode of protoberberine compounds to Gf TNMT appears to be similar to coclaurine NMT, with the isoquinoline rings buried deepest in the binding pocket. This binding mode differs from that of pavine NMT, in which the benzyl ring is bound more deeply than the isoquinoline rings. The insights into substrate recognition and catalysis provided here form a sound basis for the rational engineering of NMT enzymes for chemoenzymatic synthesis and metabolic engineering.

  • Organizational Affiliation

    Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tetrahydroprotoberberine N-methyltransferase383Glaucium flavumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAM (Subject of Investigation/LOI)
Query on SAM

Download Ideal Coordinates CCD File 
C15 H22 N6 O5 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.023α = 90
b = 104.023β = 90
c = 82.746γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-23
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description