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Information on EC 2.1.1.158 - 7-methylxanthosine synthase and Organism(s) Coffea canephora and UniProt Accession A4GE69
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2.1.1.158 7-methylxanthosine synthaseIUBMB Comments
The enzyme is specific for xanthosine, as XMP and xanthine cannot act as substrates [2,4]. The enzyme does not have N1- or N3- methylation activity . This is the first methylation step in the production of caffeine.
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Word Map
- 2.1.1.158
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histone-lysine
- histone
-
n-methylation
- methyltransferases
- phosphatidylcholine
-
euchromatic
- phosphatidylethanolamine
-
methylase
- phenylethanolamine
- s-adenosyl-l-homocysteine
-
prmts
- adomet
-
zeste
- coffea
- theobromine
- protein-arginine
-
s-adenosyl-l-methionine-dependent
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s-adenosylmethionine-dependent
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dimethylaminohydrolase
- phosphatidyl-n-monomethylethanolamine
- guanidinoacetate
- canephora
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ddahs
- agriculture
The taxonomic range for the selected organisms is: Coffea canephora
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
Synonyms
n-methyltransferase, xanthosine methyltransferase, cmxrs1, 7-n-methyltransferase, 7-methylxanthosine synthase, 7-methylxanthine synthase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + xanthosine = S-adenosyl-L-homocysteine + 7-methylxanthosine
a catalytic residue is Gln161, cosubstrate and substrate binding site structures involving the Ser316 for xanthosine recognition, overview
SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:xanthosine N7-methyltransferase
The enzyme is specific for xanthosine, as XMP and xanthine cannot act as substrates [2,4]. The enzyme does not have N1- or N3- methylation activity [2]. This is the first methylation step in the production of caffeine.
CAS REGISTRY NUMBER
COMMENTARY
192827-92-2
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + xanthosine
S-adenosyl-L-homocysteine + 7-methylxanthosine
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-
-
?
S-adenosyl-L-methionine + xanthosine
S-adenosyl-L-homocysteine + 7-methylxanthosine
-
-
-
ir
S-adenosyl-L-methionine + xanthosine
S-adenosyl-L-homocysteine + 7-methylxanthosine
-
-
-
-
?
S-adenosyl-L-methionine + xanthosine
S-adenosyl-L-homocysteine + 7-methylxanthosine
-
-
-
-
ir
S-adenosyl-L-methionine + xanthosine
S-adenosyl-L-homocysteine + 7-methylxanthosine
-
first step in caffeine biosynthesis pathway from xanthosine, reduction of the second enzyme of the pathway, 7-methylxanthine methyltransferase, EC 2.1.1.159, leads to reduced XMT1 expression
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-
ir
S-adenosyl-L-methionine + xanthosine
S-adenosyl-L-homocysteine + 7-methylxanthosine
-
step of the caffeine biosynthesis, caffeine accumulation in seeds
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-
?
additional information
?
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both xanthosine and its monoanionic form with N3 deprotonated are used as the substrates for the methylation. While the methyl group can be transferred to the monoanionic form of xanthosine with a reasonable free energy barrier (about 17 kcal/mol), this is not the case for the neutral xanthosine (barrier is about 31 kcal/mol). The hydrogen bonding and hydrophobic interactions involving the monoanionic form closely represent the corresponding interactions in the crystal structure, which seems not to be the case for the reactant complex involving the neutral xanthosine
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-
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additional information
?
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enzyme expression and activity during caffeine biosynthesis in fruits, overview
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-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + xanthosine
S-adenosyl-L-homocysteine + 7-methylxanthosine
-
-
-
ir
additional information
?
-
-
enzyme expression and activity during caffeine biosynthesis in fruits, overview
-
-
?
S-adenosyl-L-methionine + xanthosine
S-adenosyl-L-homocysteine + 7-methylxanthosine
-
first step in caffeine biosynthesis pathway from xanthosine, reduction of the second enzyme of the pathway, 7-methylxanthine methyltransferase, EC 2.1.1.159, leads to reduced XMT1 expression
-
-
ir
S-adenosyl-L-methionine + xanthosine
S-adenosyl-L-homocysteine + 7-methylxanthosine
-
step of the caffeine biosynthesis, caffeine accumulation in seeds
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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immature, ripening, and mature, enzyme expression and activity during development, overview
additional information
-
method development for somatic embryogenesis, overview
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). XMT1_COFCA
372
0
41816
Swiss-Prot
other Location (Reliability: 2)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
42000
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant wild-type and selenomethionine-labeled XMT, 23-28% PEG 3350, 0.2 M LiCl, 0.1 M Tris-HCl, pH 8.5-8.7, 2 mM DTT, 1 mM S-adenosyl-L-cysteine, and 1 mM xanthosine, 1-3 days, 20°C, X-ray diffraction structure determination and analysis at 2.8-3.0 A resolution
purified recombinant wild-type and selenomethionine-labeled XMT, 23-28% PEG 3350, 0.2 M LiCl, 0.1 M Tris-HCl, pH 8.5-8.7, 2 mM DTT, 2 mM S-adenosyl-L-cysteine, and 2 mM xanthosine, 1-3 days, 20°C, plate-like crystals, X-ray diffraction structure determination and analysis at 2.2 A resolution
using Linbro plates and the conventional hanging-drop technique, in the presence of the demethylated cofactor S-adenosyl-l-cysteine or xanthosine
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
reduction of the second enzyme of the pathway, 7-methylxanthine methyltransferase, EC 2.1.1.159, leads to reduced XMT1 expression
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged XMT1 from Escherichia coli strain BL21(DE3) to homogeneity by nickel affinity chromatography, cleavage of the His-tag with tobacco etch virus, TEV, protease, followed by gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
expression is increased in presence of methyl jasmonate. 0.5 mM salicylic acid upregulates expression, but 0.05 mM does not
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
McCarthy, A.A.; Biget, L.; Lin, C.; Petiard, V.; Tanksley, S.D.; McCarthy, J.G.
Cloning, expression, crystallization and preliminary x-ray analysis of the XMT and DXMT N-methyltransferases from Coffea canephora (robusta)
Acta Crystallogr. Sect. F
F63
304-307
2007
Coffea canephora (A4GE69)
Ogita, S.; Uefuji, H.; Morimoto, M.; Sano, H.
Application of RNAi to confirm theobromine as the major intermediate for caffeine biosynthesis in coffee plants with potential for construction of decaffeinated varieties
Plant Mol. Biol.
54
931-941
2004
Coffea arabica (Q9AVK0), Coffea arabica, Coffea canephora
McCarthy, A.A.; McCarthy, J.G.
The structure of two N-methyltransferases from the caffeine biosynthetic pathway
Plant Physiol.
144
879-889
2007
Coffea canephora (A4GE69)
Koshiro, Y.; Zheng, X.Q.; Wang, M.L.; Nagai, C.; Ashihara, H.
Changes in content and biosynthetic activity of caffeine and trigonelline during growth and ripening of Coffea arabica and Coffea canephora fruits
Plant Sci.
171
242-250
2006
Coffea canephora, Coffea arabica (Q9AVK0)
McCarthy, A.A.; Biget, L.; Lin, C.; Petiard, V.; Tanksley, S.D.; McCarthy, J.G.
Cloning, expression, crystallization and preliminary X-ray analysis of the XMT and DXMT N-methyltransferases from Coffea canephora (robusta)
Acta Crystallogr. Sect. F
63
304-307
2007
Coffea canephora (A4GE69)
Qian, P.; Guo, H.B.; Yue, Y.; Wang, L.; Yang, X.; Guo, H.
Understanding the catalytic mechanism of xanthosine methyltransferase in caffeine biosynthesis from QM/MM molecular dynamics and free energy simulations
J. Chem. Inf. Model.
56
1755-1761
2016
Coffea canephora (A4GE69)
Kumar, A.; Giridhar, P.
Salicylic acid and methyljasmonate restore the transcription of caffeine biosynthetic N-methyltransferases from a transcription inhibition noticed during late endosperm maturation in coffee
Plant Gene
4
38-44
2015
Coffea canephora (A4GE69)
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