2EG5 | pdb_00002eg5

The structure of xanthosine methyltransferase

PDB DOI: https://doi.org/10.2210/pdb2EG5/pdb

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

Deposited: 2007-02-28 Released: 2007-05-01
Deposition Author(s): McCarthy, A.A., McCarthy, J.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.284 (Depositor), 0.257 (DCC)
R-Value Work:
0.230 (Depositor)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
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.

Organizational Affiliation

European Molecular Biology Laboratory, Grenoble 38042, France. andrewmc@embl.fr

Macromolecule Content

Total Structure Weight: 170.25 kDa
Atom Count: 11,430
Modeled Residue Count: 1,377
Deposited Residue Count: 1,488
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xanthosine methyltransferase	A, B [auth C], C [auth E], D [auth G]	372	Coffea canephora	Mutation(s): 0 Gene Names: XMT1 EC: 2.1.1 (PDB Primary Data), 2.1.1.158 (UniProt)
UniProt
Find proteins for A4GE69 (Coffea canephora) Explore A4GE69 Go to UniProtKB: A4GE69
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4GE69
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain K [auth G] SDF format, chain I [auth E] SDF format, chain G [auth C] SDF format, chain E [auth A] MOL2 format, chain K [auth G] MOL2 format, chain I [auth E] MOL2 format, chain G [auth C] MOL2 format, chain E [auth A] mmCIF format, chain K [auth G] mmCIF format, chain I [auth E] mmCIF format, chain G [auth C] mmCIF format, chain E [auth A]	E [auth A], G [auth C], I [auth E], K [auth G]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain E [auth A] Focus chain G [auth C] Focus chain I [auth E] Focus chain K [auth G] Interactions & Density Focus chain E [auth A] Focus chain G [auth C] Focus chain I [auth E] Focus chain K [auth G]
XTS Query on XTS Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth G] SDF format, chain J [auth E] SDF format, chain H [auth C] MOL2 format, chain F [auth A] MOL2 format, chain L [auth G] MOL2 format, chain J [auth E] MOL2 format, chain H [auth C] mmCIF format, chain F [auth A] mmCIF format, chain L [auth G] mmCIF format, chain J [auth E] mmCIF format, chain H [auth C]	F [auth A], H [auth C], J [auth E], L [auth G]	9-[(2R,3R,4S,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)OXOLAN-2-YL]-3H-PURINE-2,6-DIONE C₁₀ H₁₂ N₄ O₆ UBORTCNDUKBEOP-BDXYJKHTSA-N		Interactions Focus chain F [auth A] Focus chain H [auth C] Focus chain J [auth E] Focus chain L [auth G] Interactions & Density Focus chain F [auth A] Focus chain H [auth C] Focus chain J [auth E] Focus chain L [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.284 (Depositor), 0.257 (DCC)
R-Value Work: 0.230 (Depositor)
R-Value Observed: 0.233 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.59	α = 90
b = 119.8	β = 102.16
c = 116.4	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-05-01

Deposition Author(s):

McCarthy, A.A.

McCarthy, J.G.

Revision History (Full details and data files)

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: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary