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EC Tree
IUBMB Comments The enzyme, characterized from the bacterium Sphingomonas sp. SYK6, is involved in the degradation of lignin. The enzyme has similar activities with vanillate and 3-O-methylgallate.
The enzyme appears in viruses and cellular organisms
Synonyms
syringate o-demethylase, tetrahydrofolate-dependent o-demethylase, vanillate/3mga o-demethylase,
more
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tetrahydrofolate-dependent O-demethylase
vanillate/3-O-methylgallate O-demethylase
vanillate/3MGA O-demethylase
DesA
Q7WST1
-
LigM
Q60FX1
-
syringate O-demethylase
Q7WST1
-
syringate O-demethylase
Q7WST1
-
-
tetrahydrofolate-dependent O-demethylase
Q60FX1
-
tetrahydrofolate-dependent O-demethylase
Q60FX1
-
-
vanillate/3-O-methylgallate O-demethylase
Q60FX1
-
vanillate/3-O-methylgallate O-demethylase
Q60FX1
-
-
vanillate/3MGA O-demethylase
Q60FX1
-
vanillate/3MGA O-demethylase
Q60FX1
-
-
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3-O-methylgallate + tetrahydrofolate = gallate + 5-methyltetrahydrofolate
(2)
-
-
-
vanillate + tetrahydrofolate = protocatechuate + 5-methyltetrahydrofolate
(1)
-
-
-
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vanillate:tetrahydrofolate O-methyltransferase
The enzyme, characterized from the bacterium Sphingomonas sp. SYK6, is involved in the degradation of lignin. The enzyme has similar activities with vanillate and 3-O-methylgallate.
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3-O-methylgallate + tetrahydrofolate
gallate + 5-methyltetrahydrofolate
dicamba + O2 + electron donor + tetrahydrofolate
? + oxidized electron donor + H2O + methyltetrahydrofolate
-
titanium III citrate can act as electron donor, inducible three-component system consisting of MtvA, MtvB and MtvC, that catalyzes methyl transfer from vanillate to tetrahydrofolate
-
-
?
syringate + 2 tetrahydrofolate
protocatechuate + 2 5-methyltetrahydrofolate
syringate + tetrahydrofolate
3-O-methylgallate + 5-methyltetrahydrofolate
vanillate + tetrahydrofolate
3,4-dihydroxybenzoate + 5-methyltetrahydrofolate
vanillate + tetrahydrofolate
protocatechuate + 5-methyltetrahydrofolate
additional information
?
-
3-O-methylgallate + tetrahydrofolate
gallate + 5-methyltetrahydrofolate
Q60FX1
-
-
-
?
3-O-methylgallate + tetrahydrofolate
gallate + 5-methyltetrahydrofolate
Q7WST1
-
0.4% of the activity with syringate
-
?
3-O-methylgallate + tetrahydrofolate
gallate + 5-methyltetrahydrofolate
Q7WST1
-
0.4% of the activity with syringate
-
?
syringate + 2 tetrahydrofolate
protocatechuate + 2 5-methyltetrahydrofolate
Q60FX1
-
-
-
?
syringate + 2 tetrahydrofolate
protocatechuate + 2 5-methyltetrahydrofolate
Q60FX1
-
-
-
?
syringate + tetrahydrofolate
3-O-methylgallate + 5-methyltetrahydrofolate
Q7WST1
-
-
-
?
syringate + tetrahydrofolate
3-O-methylgallate + 5-methyltetrahydrofolate
Q7WST1
-
-
-
?
vanillate + tetrahydrofolate
3,4-dihydroxybenzoate + 5-methyltetrahydrofolate
-
-
-
-
?
vanillate + tetrahydrofolate
3,4-dihydroxybenzoate + 5-methyltetrahydrofolate
-
titanium III citrate can act as electron donor, inducible three-component system consisting of MtvA, MtvB and MtvC, that catalyzes methyl transfer from vanillate to tetrahydrofolate
-
-
?
vanillate + tetrahydrofolate
protocatechuate + 5-methyltetrahydrofolate
-
-
-
?
vanillate + tetrahydrofolate
protocatechuate + 5-methyltetrahydrofolate
Q60FX1
-
-
-
?
vanillate + tetrahydrofolate
protocatechuate + 5-methyltetrahydrofolate
Q60FX1
-
procatechuic acid is 3,4-dihydroxybenzoate, procatechuic acid is 3,4-dihydroxybenzoate, which is further degraded via the procatechiuc acid 4,5-cleavage pathway
-
?
vanillate + tetrahydrofolate
protocatechuate + 5-methyltetrahydrofolate
Q7WST1
-
3% of the activity with syringate
-
?
vanillate + tetrahydrofolate
protocatechuate + 5-methyltetrahydrofolate
Q60FX1
-
procatechuic acid is 3,4-dihydroxybenzoate, procatechuic acid is 3,4-dihydroxybenzoate, which is further degraded via the procatechiuc acid 4,5-cleavage pathway
-
?
vanillate + tetrahydrofolate
protocatechuate + 5-methyltetrahydrofolate
-
-
procatechuic acid is 3,4-dihydroxybenzoate, which is further degraded via the procatechiuc acid 4,5-cleavage pathway
-
?
vanillate + tetrahydrofolate
protocatechuate + 5-methyltetrahydrofolate
Q60FX1
-
-
-
?
vanillate + tetrahydrofolate
protocatechuate + 5-methyltetrahydrofolate
Q7WST1
-
3% of the activity with syringate
-
?
additional information
?
-
Q60FX1
syringate is no substrate
-
-
?
additional information
?
-
Q60FX1
enzyme uses an ordered sequential mechanism
-
-
?
additional information
?
-
Q60FX1
no requirement for ATP
-
-
?
additional information
?
-
Q60FX1
no substrate: syringate
-
-
?
additional information
?
-
Q60FX1
syringate is no substrate
-
-
?
additional information
?
-
-
syringate is no substrate
-
-
?
additional information
?
-
Q60FX1
no substrate: syringate
-
-
?
additional information
?
-
-
no substrate: syringate
-
-
?
additional information
?
-
Q60FX1
no requirement for ATP
-
-
?
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syringate + tetrahydrofolate
3-O-methylgallate + 5-methyltetrahydrofolate
vanillate + tetrahydrofolate
3,4-dihydroxybenzoate + 5-methyltetrahydrofolate
-
-
-
-
?
vanillate + tetrahydrofolate
protocatechuate + 5-methyltetrahydrofolate
syringate + tetrahydrofolate
3-O-methylgallate + 5-methyltetrahydrofolate
Q7WST1
-
-
-
?
syringate + tetrahydrofolate
3-O-methylgallate + 5-methyltetrahydrofolate
Q7WST1
-
-
-
?
vanillate + tetrahydrofolate
protocatechuate + 5-methyltetrahydrofolate
Q60FX1
-
procatechuic acid is 3,4-dihydroxybenzoate, which is further degraded via the procatechiuc acid 4,5-cleavage pathway
-
?
vanillate + tetrahydrofolate
protocatechuate + 5-methyltetrahydrofolate
Q60FX1
-
procatechuic acid is 3,4-dihydroxybenzoate, which is further degraded via the procatechiuc acid 4,5-cleavage pathway
-
?
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tetrahydrofolate
Q60FX1
-
tetrahydrofolate
Q7WST1
-
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5-methyltetrahydrofolate
Q60FX1
competitive with respect to tetrahydrofolate, noncompetitive with respect to vanillate
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tetrahydrofolate
Q60FX1
dependent on
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0.72
tetrahydrofolate
Q60FX1
pH 8.0, 30°C
0.078
vanillate
wild-type, pH 8.0, 30°C
0.085
vanillate
-
55°C, pH 6.6
0.63
vanillate
Q60FX1
pH 8.0, 30°C
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0.385
vanillate
wild-type, pH 8.0, 30°C
5.76
vanillate
Q60FX1
pH 8.0, 30°C
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8
tetrahydrofolate
Q60FX1
pH 8.0, 30°C
9.14
vanillate
Q60FX1
pH 8.0, 30°C
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0.1 - 0.17
5-methyltetrahydrofolate
0.1
5-methyltetrahydrofolate
Q60FX1
substrate vanillate, pH 8.0, 30°C
0.17
5-methyltetrahydrofolate
Q60FX1
substrate tetrahydrofolate, pH 8.0, 30°C
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8
Q60FX1
-
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30
Q60FX1
-
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-
-
-
brenda
-
UniProt
brenda
-
Q60FX1
SwissProt
brenda
-
Q7WST1
UniProt
brenda
-
Q60FX1
SwissProt
brenda
gene ligM
Q60FX1
SwissProt
brenda
-
Q60FX1
SwissProt
brenda
-
Q7WST1
UniProt
brenda
gene ligM
Q60FX1
SwissProt
brenda
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physiological function
Q7WST1
disruption of DesA results in a growth defect on syringate but does not affect growth on vanillate
physiological function
Q60FX1
disruption of LigM leads to significant growth retardation on both vanillate and syringate. The ability of the mutant to transform vanillate is markedly decreased, and it completely lost the 3-O-methylgallate O-demethylase activity. A LigM syringate demethylase DesA double mutant completely lost the ability to transform vanillate
physiological function
Q60FX1
overview on the degradation pathway of various lignin-related compounds
physiological function
-
disruption of LigM leads to significant growth retardation on both vanillate and syringate. The ability of the mutant to transform vanillate is markedly decreased, and it completely lost the 3-O-methylgallate O-demethylase activity. A LigM syringate demethylase DesA double mutant completely lost the ability to transform vanillate
-
physiological function
-
overview on the degradation pathway of various lignin-related compounds
-
physiological function
-
disruption of DesA results in a growth defect on syringate but does not affect growth on vanillate
-
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LIGM_SPHSK
Sphingobium sp. (strain NBRC 103272 / SYK-6)
471
0
52325
Swiss-Prot
-
A0A653U1F3_9MICC
475
0
52999
TrEMBL
-
A0A653LFI5_9MICC
470
0
52092
TrEMBL
-
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60000
Q60FX1
x * 60000, SDS-PAGE
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dimer
2 * 52300, calculated
?
Q60FX1
x * 60000, SDS-PAGE
?
Q7WST1
x * 50721, calulated
?
-
x * 60000, SDS-PAGE
-
?
-
x * 50721, calulated
-
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structure of apo form and in complex with substrates and tetrahydrofolate. Residues His60 and Tyr247 are essential to the catalytic activity of LigM. Their interactions with the oxygen atom in the methoxy group of vanillate seem to facilitate a methyl moiety transfer to tetrahydrofolate
to 1.81 A resolution, structure reveals a unique demethylase fold and a canonical folate-binding domain
Q60FX1
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H60A
loss of catalytic activity, mutant is able to bind both substrates
Y247F
loss of catalytic activity, mutant is able to bind both substrates
Y31A
loss of catalytic activity
H60A
Q60FX1
97-99% loss of activity
M61A
Q60FX1
97-99% loss of activity
R122A
Q60FX1
97-99% loss of activity
R122A/R147A
Q60FX1
complete loss of activity
Y247F
Q60FX1
almost complete loss of activity, no discernible effect on overall protein fold or solution behavior
Y29A
Q60FX1
97-99% loss of activity
Y31A
Q60FX1
97-99% loss of activity
additional information
Q60FX1
disruption of ligM leads to significant growth retardation on both vanillate and syringate, a ligM desA double mutant completely looses the ability to transform vanillate, phenotypes, overview
additional information
-
disruption of ligM leads to significant growth retardation on both vanillate and syringate, a ligM desA double mutant completely looses the ability to transform vanillate, phenotypes, overview
-
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expression in Escherichia coli
gene ligM, DNA and amino acid sequence determination and analysis, functional expression in Escherichia coli strains JM109 and BL21(DE3)
Q60FX1
expression in Escherichia coli
Q60FX1
expression in Escherichia coli
Q7WST1
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Naidu, D.; Ragsdale, S.W.
Characterization of a three-component vanillate O-demethylase from Moorella thermoacetica
J. Bacteriol.
183
3276-3281
2001
Moorella thermoacetica
brenda
Abe, T.; Masai, E.; Miyauchi, K.; Katayama, Y.; Fukuda, M.
A tetrahydrofolate-dependent O-demethylase, LigM, is crucial for catabolism of vanillate and syringate in Sphingomonas paucimobilis SYK-6
J. Bacteriol.
187
2030-2037
2005
Sphingomonas paucimobilis (Q60FX1), Sphingomonas paucimobilis SYK-6 (Q60FX1), Sphingomonas paucimobilis SYK-6
brenda
Nishikawa, S.; Sonoki, T.; Kasahara, T.; Obi, T.; Kubota, S.; Kawai, S.; Morohoshi, N.; Katayama, Y.
Cloning and sequencing of the Sphingomonas (Pseudomonas) paucimobilis gene essential for the O demethylation of vanillate and syringate
Appl. Environ. Microbiol.
64
836-842
1998
Sphingomonas paucimobilis (Q60FX1), Sphingomonas paucimobilis SYK-6 (Q60FX1)
brenda
Harada, A.; Kamimura, N.; Takeuchi, K.; Yu, H.Y.; Masai, E.; Senda, T.
The crystal structure of a new O-demethylase from Sphingobium sp. strain SYK-6
FEBS J.
284
1855-1867
2017
Sphingobium sp. (G2IQS7)
brenda
Masai, E.; Sasaki, M.; Minakawa, Y.; Abe, T.; Sonoki, T.; Miyauchi, K.; Katayama, Y.; Fukuda, M.
A novel tetrahydrofolate-dependent O-demethylase gene is essential for growth of Sphingomonas paucimobilis SYK-6 with syringate
J. Bacteriol.
186
2757-2765
2004
Sphingomonas paucimobilis (Q7WST1), Sphingomonas paucimobilis SYK-6 (Q7WST1), Sphingomonas paucimobilis SYK-6
brenda
Kohler, A.C.; Mills, M.J.L.; Adams, P.D.; Simmons, B.A.; Sale, K.L.
Structure of aryl O-demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism
Proc. Natl. Acad. Sci. USA
114
E3205-E3214
2017
Sphingomonas paucimobilis (Q60FX1)
brenda
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