6GKZ

Crystal structure of Coclaurine N-Methyltransferase (CNMT) bound to N-methylheliamine and SAH

• PDB DOI:  https://doi.org/10.2210/pdb6GKZ/pdb

• Classification: TRANSFERASE
• Organism(s): Coptis japonica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-22 Released: 2019-01-16 
• Deposition Author(s): Dunstan, M.S., Levy, C.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.243 
• R-Value Work: 0.165 
• R-Value Observed: 0.168 

Literature

Structure and Biocatalytic Scope of Coclaurine N-Methyltransferase.

Bennett, M.R., Thompson, M.L., Shepherd, S.A., Dunstan, M.S., Herbert, A.J., Smith, D.R.M., Cronin, V.A., Menon, B.R.K., Levy, C., Micklefield, J.

(2018) Angew Chem Int Ed Engl 57: 10600-10604

• PubMed: 29791083 
• DOI: https://doi.org/10.1002/anie.201805060
• Primary Citation of Related Structures:  
  6GKV, 6GKY, 6GKZ


• PubMed Abstract: 
  

Benzylisoquinoline alkaloids (BIAs) are a structurally diverse family of plant secondary metabolites, which have been exploited to develop analgesics, antibiotics, antitumor agents, and other therapeutic agents. Biosynthesis of BIAs proceeds via a common pathway from tyrosine to (S)-reticulene at which point the pathway diverges. Coclaurine N-methyltransferase (CNMT) is a key enzyme in the pathway to (S)-reticulene, installing the N-methyl substituent that is essential for the bioactivity of many BIAs. In this paper, we describe the first crystal structure of CNMT which, along with mutagenesis studies, defines the enzymes active site architecture. The specificity of CNMT was also explored with a range of natural and synthetic substrates as well as co-factor analogues. Knowledge from this study could be used to generate improved CNMT variants required to produce BIAs or synthetic derivatives.

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Organizational Affiliation: 

School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 167.88 kDa 
• Atom Count: 11,438 
• Modelled Residue Count: 1,346 
• Deposited Residue Count: 1,404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coclaurine N-methyltransferase	A, B, C, D	351	Coptis japonica	Mutation(s): 0  Gene Names: cnmt EC: 2.1.1.115

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	E [auth A], F [auth B], G [auth C], H [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.243 
• R-Value Work: 0.165 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.75	α = 90
b = 203.43	β = 90
c = 54.54	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Dunstan, M.S., Levy, C.W.

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Funding Organization	Location	Grant Number
	United Kingdom	--

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release