Information on EC 6.2.1.44 - 3-(methylthio)propionyl-CoA ligase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
6.2.1.44
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RECOMMENDED NAME
GeneOntology No.
3-(methylthio)propionyl-CoA ligase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + 3-(methylthio)propanoate + CoA = AMP + diphosphate + 3-(methylthio)propanoyl-CoA
show the reaction diagram
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
methylthiopropanoate degradation I (cleavage)
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Sulfur metabolism
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SYSTEMATIC NAME
IUBMB Comments
3-(methylthio)propanoate:CoA ligase (AMP-forming)
The enzyme is part of a dimethylsulfoniopropanoate demethylation pathway in the marine bacteria Ruegeria pomeroyi and Pelagibacter ubique. It also occurs in some nonmarine bacteria capable of metabolizing dimethylsulfoniopropionate (e.g. Burkholderia thailandensis, Pseudomonas aeruginosa, and Silicibacter lacuscaerulensis). It requires Mg2+ [2].
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
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growth of a dmdB mutant (SPO2045::tet) is somewhat delayed during growth on 3-(methylthio)propionate. Following growth with 3-(dimethylsulphonio)propanoate, the DmdB activity is reduced by only 40% compared to the wild-type
metabolism
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ATP + 3-(methylthio)propanoate + CoA
AMP + diphosphate + 3-(methylthio)propionyl-CoA
show the reaction diagram
ATP + 3-(methylthio)propanoate + CoA
AMP + diphosphate + 3-methylmercaptopropionyl-CoA
show the reaction diagram
once released from phytoplankton, marine bacteria degrade dimethylsulfoniopropionate by either the cleavage pathway to form the volatile gas dimethylsulfide or the demethylation pathway, yielding methanethiol, which is readily assimilated or oxidized. The enzyme DmdB, a methylmercaptopropionate-coenzyme A ligase, catalyzes the second step in the demethylation pathway and is a major regulatory point. Two forms of DmdB are present in the marine roseobacter Ruegeria pomeroyi DSS-3, RPO_DmdB1 and RPO_DmdB2
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-
?
ATP + 3-methylbutanoate + CoA
AMP + diphosphate + 3-methylbutanoyl-CoA
show the reaction diagram
ATP + acetate + CoA
AMP + diphosphate + acetyl-CoA
show the reaction diagram
ATP + acrylate + CoA
AMP + diphosphate + acryloyl-CoA
show the reaction diagram
ATP + butyrate + CoA
AMP + diphosphate + butyryl-CoA
show the reaction diagram
ATP + crotonate + CoA
AMP + diphosphate + crotonyl-CoA
show the reaction diagram
ATP + hexanoate + CoA
AMP + diphosphate + hexanoyl-CoA
show the reaction diagram
ATP + isobutyrate + CoA
AMP + diphosphate + isobutyryl-CoA
show the reaction diagram
ATP + methylbutyrate + CoA
AMP + diphosphate + methylbutyryl-CoA
show the reaction diagram
ATP + pentanoate + CoA
AMP + diphosphate + pentanoyl-CoA
show the reaction diagram
ATP + propionate + CoA
AMP + diphosphate + propionyl-CoA
show the reaction diagram
additional information
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + 3-(methylthio)propanoate + CoA
AMP + diphosphate + 3-(methylthio)propionyl-CoA
show the reaction diagram
ATP + 3-(methylthio)propanoate + CoA
AMP + diphosphate + 3-methylmercaptopropionyl-CoA
show the reaction diagram
Q5LRT0, Q5LVM3
once released from phytoplankton, marine bacteria degrade dimethylsulfoniopropionate by either the cleavage pathway to form the volatile gas dimethylsulfide or the demethylation pathway, yielding methanethiol, which is readily assimilated or oxidized. The enzyme DmdB, a methylmercaptopropionate-coenzyme A ligase, catalyzes the second step in the demethylation pathway and is a major regulatory point. Two forms of DmdB are present in the marine roseobacter Ruegeria pomeroyi DSS-3, RPO_DmdB1 and RPO_DmdB2
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
(NH4)2SO4
0.4 M, 1.5fold enhancement of activity
KCl
0.4 M, 1.4fold enhancement of activity
Na2SO4
0.4 M, 1.2fold enhancement of activity
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(NH4)2SO4
dimethylsulfoniopropionate
inhibited by physiological concentrations (70 mM). ADP reverses the inhibition of RPO_DmdB1, suggesting that this enzyme was responsive to cellular energy charge; inhibited by physiological concentrations (70 mM). ADP reverses the inhibition of RPO_DmdB1, suggesting that this enzyme was responsive to cellular energy charge. 3-(Methylthio)propanoate reverses the inhibition of RPO_DmdB2, suggesting that a complex regulatory system exists
K2SO4
Li2SO4
Na2SO4
NH4Cl
potassium acetate
Sodium acetate
additional information
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.04 - 0.08
3-(methylthio)propanoate
0.44 - 5.25
Acrylate
0.01 - 2
Butyrate
0.04 - 3.11
propionate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
14.9 - 29.4
3-(methylthio)propanoate
1 - 22.3
Acrylate
7.2 - 43.8
Butyrate
3.7 - 17.7
propionate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
213 - 735
3-(methylthio)propanoate
13825
0.2 - 50
Acrylate
1915
71 - 3370
Butyrate
462
1.2 - 505
propionate
312
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.118
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chemostat, pH and temperature not specified in the publication
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
10 - 30
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
58000
2 * 58000, SDS-PAGE
59000
2 * 59000, SDS-PAGE
59143
x * 59143, calculated from sequence
59166
2 * 59166, calculated from sequence
59400
x * 59400, calculated from sequence
59548
x * 59548, calculated from sequence
61340
2 * 61340, calculated from sequence
62000
2 * 62000, SDS-PAGE
64781
x * 64781, calculated from sequence
112000
gel filtration
122000
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, stable in 100 mM HEPES for up to 6 months
-20C, stable in a solution of 100 mM KHPO4 for up to 2 months
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
expression in Escherichia coli; expression in Escherichia coli
the dmdB gene is cloned into the pET101 expression vector and expressed in Escherichia coli, and the recombinant Escherichia coli strain possesses 3-(methylthio)propionyl-CoA ligase activity, whereas the host strain alone does not
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
the amount of transcripts for dmdB, dmdC and dmdD increases during growth of wild-type enzyme on 3-(methylthio)propanoate or 3-(dimethylsulphonio)propanoate, as expected if the pathway is required for 3-(methylthio)propanoate metabolism
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two forms of DmdB are present in the marine roseobacter Ruegeria pomeroyi DSS-3, RPO_DmdB1 and RPO_DmdB2. They are differentially expressed depending on carbon source. RPO_dmdB1 exhibits overall lower steady-state levels of mRNA than RPO_dmdB2 for dimethylsulfoniopropionate, 3-(methylthio)propanoate, or methionine as the sole source of carbon. Although the levels of the RPO_dmdB1 transcripts increases during growth on dimethylsulfoniopropionate and methionine, it is always lower than those of RPO_dmdB2. For that reason, RPO_dmdB2 appears to be the major DmdB during growth on compounds leading to 3-(methylthio)propanoate formation; two forms of DmdB are present in the marine roseobacter Ruegeria pomeroyi DSS-3, RPO_DmdB1 and RPO_DmdB2. They are differentially expressed depending on carbon source. RPO_dmdB1 exhibits overall lower steady-state levels of mRNA than RPO_dmdB2 for dimethylsulfoniopropionate, 3-(methylthio)propanoate, or methionine as the sole source of carbon. Although the levels of the RPO_dmdB1 transcripts increases during growth on dimethylsulfoniopropionate and methionine, it is always lower than those of RPO_dmdB2. For that reason, RPO_dmdB2 appears to be the major DmdB during growth on compounds leading to 3-(methylthio)propanoate formation