2EFJ | pdb_00002efj

The structure of 1,7 dimethylxanthine methyltransferase

• PDB DOI: https://doi.org/10.2210/pdb2EFJ/pdb

• Classification: TRANSFERASE
• Organism(s): Coffea canephora
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-02-22 Released: 2007-05-01 
• Deposition Author(s): McCarthy, A.A., McCarthy, J.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.276 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.212 (DCC) 

Literature

The structure of two N-methyltransferases from the caffeine biosynthetic pathway

McCarthy, A.A., McCarthy, J.G.

(2007) Plant Physiol 144: 879-889

• PubMed: 17434991 
• DOI: https://doi.org/10.1104/pp.106.094854
• Primary Citation Related Structures: 
  2EFJ, 2EG5


• PubMed Abstract: 
  

  Caffeine (1,3,7-trimethylxanthine) is a secondary metabolite produced by certain plant species and an important component of coffee (Coffea arabica and Coffea canephora) and tea (Camellia sinensis). Here we describe the structures of two S-adenosyl-l-methionine-dependent N-methyltransferases that mediate caffeine biosynthesis in C. canephora 'robusta', xanthosine (XR) methyltransferase (XMT), and 1,7-dimethylxanthine methyltransferase (DXMT). Both were cocrystallized with the demethylated cofactor, S-adenosyl-L-cysteine, and substrate, either xanthosine or theobromine. Our structures reveal several elements that appear critical for substrate selectivity. Serine-316 in XMT appears central to the recognition of XR. Likewise, a change from glutamine-161 in XMT to histidine-160 in DXMT is likely to have catalytic consequences. A phenylalanine-266 to isoleucine-266 change in DXMT is also likely to be crucial for the discrimination between mono and dimethyl transferases in coffee. These key residues are probably functionally important and will guide future studies with implications for the biosynthesis of caffeine and its derivatives in plants.

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Organizational Affiliation: 
• European Molecular Biology Laboratory, Grenoble 38042, France. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 43.97 kDa 
• Atom Count: 2,931 
• Modeled Residue Count: 348 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3,7-dimethylxanthine methyltransferase	A	384	Coffea canephora	Mutation(s): 0  Gene Names: DXMT1 EC: 2.1.1 (PDB Primary Data), 2.1.1.160 (UniProt)
UniProt
Find proteins for A4GE70 (Coffea canephora) Explore A4GE70  Go to UniProtKB:  A4GE70

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
37T	C [auth A]	THEOBROMINE C7 H8 N4 O2 YAPQBXQYLJRXSA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.276 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.212 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.16	α = 90
b = 105.63	β = 90
c = 140.95	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-01 
Deposition Author(s): McCarthy, A.A., McCarthy, J.G.

Revision History  

• Version 1.0: 2007-05-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations, Structure summary