Information on EC 2.1.1.269 - dimethylsulfoniopropionate demethylase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
2.1.1.269
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RECOMMENDED NAME
GeneOntology No.
dimethylsulfoniopropionate demethylase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
S,S-dimethyl-beta-propiothetin + tetrahydrofolate = 3-(methylthio)propanoate + 5-methyltetrahydrofolate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
demethylation
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
dimethylsulfoniopropanoate degradation III (demethylation)
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Sulfur metabolism
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SYSTEMATIC NAME
IUBMB Comments
S,S-dimethyl-beta-propiothetin:tetrahydrofolate S-methyltransferase
The enzyme from the marine bacteria Pelagibacter ubique and Ruegeria pomeroyi are specific towards S,S-dimethyl-beta-propiothetin. They do not demethylate glycine-betaine [1,2].
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
in phytoplankton bloom in Gulf of Mexico seawater, gene dmdA, genetic cluster identification from 578 dmdA sequences
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Manually annotated by BRENDA team
in phytoplankton bloom in Gulf of Mexico seawater, gene dmdA, OM60 group, genetic cluster OM60-like identification from 578 dmdA sequences
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Manually annotated by BRENDA team
in phytoplankton bloom in Gulf of Mexico seawater, gene dmdA, clade A, genetic cluster identification from 578 dmdA sequences
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Manually annotated by BRENDA team
Roseobacter sp.
from Monterey Bay, Canada, gene dmdA
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Manually annotated by BRENDA team
in phytoplankton bloom in Gulf of Mexico seawater, gene dmdA, OM60 group, genetic cluster OM60-like identification from 578 dmdA sequences
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Manually annotated by BRENDA team
pelagibacteraceae, strains HTCC1002 and HTCC1062, in phytoplankton bloom in Gulf of Mexico seawater, gene dmdA, OM60 group, clade E, genetic cluster identification from 578 dmdA sequences
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Manually annotated by BRENDA team
pelagibacteraceae, strains HTCC1002 and HTCC1062, in phytoplankton bloom in Gulf of Mexico seawater, gene dmdA, OM60 group, clade E, genetic cluster identification from 578 dmdA sequences
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
metabolism
physiological function
additional information
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positive correlation of katG expression with gene dmdA but not gene dddP during the period when regulation expression is uncoupled
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2-(dimethylsulfonio)propanoate + tetrahydrofolate
2-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate
show the reaction diagram
3-(S,S-dimethylsulfonio)propanoate + tetrahydrofolate
3-(methylthio)propanoate + 5-methyltetrahydrofolate
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
2-(dimethylsulfonio)propanoate + tetrahydrofolate
2-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate
show the reaction diagram
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?
additional information
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
tetrahydrofolate
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3-(methylthio)propanoate
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dimethylsulfoniobutanoate
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substrate analog, weak inhibitor
dimethylsulfoniopentanoate
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substrate analog, weak inhibitor
methylmercaptopropionate
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product inhibition
MgCl2
O2
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preincubation of the extract under air decreases the activity, 35% loss in 3 h
Propyl iodide
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0.5 mM, complete inhibition. In the light, the inhibition is far less strong
additional information
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5.4 - 13.2
3-(S,S-dimethylsulfonio)propanoate
8.6 - 13.2
dimethylsulfoniopropionate
0.21 - 0.29
tetrahydrofolate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.4 - 8.1
3-(S,S-dimethylsulfonio)propanoate
8.1
dimethylsulfoniopropionate
Candidatus Pelagibacter ubique
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.45 - 0.618
3-(S,S-dimethylsulfonio)propanoate
19731
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.1
3-(methylthio)propanoate
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.2
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assay at
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 8.8
maximum activity is observed at pH 7.0 to 8.0, about 50% activity at pH 6.0 and 8.8; more than 50% of maximum activity within
6.5 - 8.3
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maximum activity is observed at pH 7.0 to 8.0, about 50% activity at pH 6.5 and 8.3; more than 50% of maximum activity within
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Pelagibacter ubique (strain HTCC1062)
Pelagibacter ubique (strain HTCC1062)
Pelagibacter ubique (strain HTCC1062)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
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structure of apoenzyme DmdA and domain architecture, overview
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
purified recombinant DmdA alone or in complex with substrate 2-(dimethylsulfonio)propanoate or cofactor tetrahydrofolate, mother liquor consists of 325 mM NaCl, 30% PEG 2000, 25 mM HEPES, pH 6.8. method optimization, soaking in solution containing 2 mM DMSP or 2 mM tetrahydrofolate, X-ray diffraction structure determination and analysis at 2.1 A and 1.6 A resolution, respectively, modeling; structure of the apoenzyme DmdA to 2.1 A, as well as for co-crystals soaked with substrate dimethylsulfoniopropionate to 1.6 A or the cofactor tetrahydrofolate to 1.6 A. The overall fold is a triple domain structure similar to what has been observed for the glycine cleavage T protein or sarcosine oxidase. The tetrahydrofolate binding fold appears conserved
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
anion-exchange, hydrophobic interaction, and hydroxyapatite chromatographies; recombinant protein
recombinant DmdA from Escherichia coli
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
gene dmdA, expression in Escherichia coli
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gene dmdA, genetic cluster identification from 578 dmdA sequences from seawater plankton probes, DNA and amino acid sequence determination and analysis, phylogenetic analysis
gene dmdA, genotyping and expression analysis
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gene dmdA, genotyping and expression analysis in relation to the phytoplankton dynamics in Monterey Bay
Roseobacter sp.
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gene dmdA, genotyping in marine bacteria, overview
synthesized and introduced in trans into Escherichia coli
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