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Information on EC 2.1.1.269 - dimethylsulfoniopropionate demethylase and Organism(s) Ruegeria pomeroyi and UniProt Accession Q5LS57
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2.1.1.269 dimethylsulfoniopropionate demethylaseIUBMB Comments
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].
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Word Map
- 2.1.1.269
- sulfur
-
demethylation
-
ocean
-
phytoplankton
- roseobacter
- clade
- dimethylsulfide
-
bacterioplankton
- sulfide
-
climatically
- seawater
-
algal
-
metagenomic
-
pacific
- atmosphere
-
coastal
- pomeroyi
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subclade
-
pelagibacter
- ubique
- lyases
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free-living
The taxonomic range for the selected organisms is: Ruegeria pomeroyi
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
Synonyms
dmsp demethylase, dimethylsulfoniopropionate demethylase, dmsp methyltransferase, dimethylsufoniopropionate-dependent demethylase a, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
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].
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
2-(dimethylsulfonio)propanoate + tetrahydrofolate
2-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate
enzyme exhibits strict substrate specificity for 2-(dimethylsulfonio)propanoate
-
-
?
3-(S,S-dimethylsulfonio)propanoate + tetrahydrofolate
3-(methylthio)propanoate + 5-methyltetrahydrofolate
-
-
-
?
S,S-dimethyl-beta-propiothetin + tetrahydrofolate
3-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate
-
-
-
?
additional information
?
-
no detectable demethylase activity with glycine betaine, dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate. Less than 1% activity is found with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate
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-
?
additional information
?
-
-
no detectable demethylase activity with glycine betaine, dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate. Less than 1% activity is found with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate
-
-
?
additional information
?
-
strict substrate specificity for dimethylsulfoniopropionate. No detectable demethylase activity with glycine betaine, dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate and less than 1% activity with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate
-
-
?
additional information
?
-
-
strict substrate specificity for dimethylsulfoniopropionate. No detectable demethylase activity with glycine betaine, dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate and less than 1% activity with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate
-
-
?
additional information
?
-
assay metod, overview. The substrate THF and product 5-methyl-THF are labile under aerobic conditions, oxidation of THF is irreversible and results in the release of 4-aminobenzoyl glutamate, essentially breaking the molecule in half. Half-life of THF in solution at pH 7.0 is about 40 min. DTT can stabilize THF in solution
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-
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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,S-dimethyl-beta-propiothetin + tetrahydrofolate
3-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
tetrahydrofolate
(DMSP) demethylase is a tetrahydrofolate-dependent enzyme
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
salt solutions do not significantly stimulate activity nor are they required for enzyme stability during storage
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
not inhibitory: 400 mM of (NH4)2SO4, K2HPO4, MgSO4, Na-acetate, NaCl, and KCl
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additional information
-
not inhibitory: 400 mM of (NH4)2SO4, K2HPO4, MgSO4, Na-acetate, NaCl, and KCl
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
5.4
3-(S,S-dimethylsulfonio)propanoate
pH 7.5, temperature not specified in the publication
0.21
tetrahydrofolate
pH 7.5, temperature not specified in the publication
8.6
dimethylsulfoniopropionate
in cell extracts, similar to that of purified recombinant DmdA
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2.4
3-(S,S-dimethylsulfonio)propanoate
pH 7.5, temperature not specified in the publication
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.45
3-(S,S-dimethylsulfonio)propanoate
pH 7.5, temperature not specified in the publication
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7 - 8
7 - 8
enzyme is more active in HEPES than in MOPS buffer, but the activities in HEPES and Tris-HCl buffers are the same
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6 - 8.8
6 - 8.8
maximum activity is observed at pH 7.0 to 8.0, about 50% activity at pH 6.0 and 8.8
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
though DmdA is homologous to the glycine cleavage T-protein and shares structural similarity, the mechanism of carbon transfer is more similar to S-adenosyl-methionine (SAM)-dependent methyl-transfer enzymes. DmdA catalyzes the transfer of a methyl group to form 5-methyl-THF, which is analogous to SAM-dependent reactions. The gene dmdA is abundant in marine waters
metabolism
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the bacterial switch is a proposed regulatory point in the global sulfur cycle that routes dimethylsulfoniopropionate to two fundamentally different fates in seawater through genes encoding either the cleavage or demethylation pathway, and affects the flux of volatile sulfur from ocean surface waters to the atmosphere
physiological function
dimethylsulfoniopropionate (DMSP) demethylase is a tetrahydrofolate-dependent enzyme that initiates the DMSP demethylation pathway in marine bacteria. This enzyme is important for understanding of organic sulfur flux from the oceans because it directs the sulfur from DMSP away from dimethylsulfide
additional information
-
positive correlation of katG expression with gene dmdA but not gene dddP during the period when regulation expression is uncoupled
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
salt solutions do not significantly stimulate activity nor are they required for enzyme stability during storage
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, enzyme in cell-free extract, in presence of EDTA and 20% glycerol, several weeks without significant loss of activity
4°C, enzyme in cell-free extract, in presence of EDTA, several weeks without significant loss of activity. Without addition of EDTA, the enzyme loses all activity over the course of several days
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
anion-exchange, hydrophobic interaction, and hydroxyapatite chromatographies
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Reisch, C.R.; Moran, M.A.; Whitman, W.B.
Dimethylsulfoniopropionate-dependent demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi
J. Bacteriol.
190
8018-8024
2008
Candidatus Pelagibacter ubique, Candidatus Pelagibacter ubique (Q4FP21), Candidatus Pelagibacter ubique HTCC1062, Candidatus Pelagibacter ubique HTCC1062 (Q4FP21), Ruegeria pomeroyi (Q5LS57), Ruegeria pomeroyi
Varaljay, V.A.; Robidart, J.; Preston, C.M.; Gifford, S.M.; Durham, B.P.; Burns, A.S.; Ryan, J.P.; Marin, R.; Kiene, R.P.; Zehr, J.P.; Scholin, C.A.; Moran, M.A.
Single-taxon field measurements of bacterial gene regulation controlling DMSP fate
ISME J.
9
1677-1686
2015
Roseobacter sp., Roseobacter sp. HTCC 2255, Ruegeria pomeroyi
Reisch, C.R.
Assay and analysis of dimethylsulfoniopropionate demethylase
Methods Enzymol.
605
325-333
2018
Candidatus Pelagibacter ubique (Q4FP21), Candidatus Pelagibacter ubique HTCC1062 (Q4FP21), Ruegeria pomeroyi (Q5LS57), Ruegeria pomeroyi ATCC 700808 (Q5LS57), Ruegeria pomeroyi DSM 15171 (Q5LS57)
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