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show all sequences of 2.1.1.269

Structures of dimethylsulfoniopropionate-dependent demethylase from the marine organism Pelagabacter ubique

Schuller, D.J.; Reisch, C.R.; Moran, M.A.; Whitman, W.B.; Lanzilotta, W.N.; Protein Sci. 21, 289-298 (2012)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
gene dmdA, expression in Escherichia coli
Candidatus Pelagibacter ubique
Crystallization (Commentary)
Crystallization
Organism
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
Candidatus Pelagibacter ubique
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
2-(dimethylsulfonio)propanoate + tetrahydrofolate
Candidatus Pelagibacter ubique
-
2-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Candidatus Pelagibacter ubique
-
gene dmda or SAR11_0246
-
Candidatus Pelagibacter ubique
Q4FP21
-
-
Candidatus Pelagibacter ubique HTCC1062
Q4FP21
-
-
Purification (Commentary)
Commentary
Organism
recombinant DmdA from Escherichia coli
Candidatus Pelagibacter ubique
Reaction
Reaction
Commentary
Organism
S,S-dimethyl-beta-propiothetin + tetrahydrofolate = 3-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate
concerted mechanism in which methyl transfer is coupled to proton transfer; DmdA catalyzes a redox-neutral methyl transfer reaction to produce 5-methyltetrahydrofolate, mechanism, overview
Candidatus Pelagibacter ubique
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2-(dimethylsulfonio)propanoate + tetrahydrofolate
-
720998
Candidatus Pelagibacter ubique
2-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate
-
-
-
?
2-(dimethylsulfonio)propanoate + tetrahydrofolate
DmdA catalyzes a redox-neutral methyl transfer reaction to produce 5-methyltetrahydrofolate
720998
Candidatus Pelagibacter ubique
2-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate
-
-
-
?
Subunits
Subunits
Commentary
Organism
More
structure of apoenzyme DmdA and domain architecture, overview
Candidatus Pelagibacter ubique
Cofactor
Cofactor
Commentary
Organism
Structure
tetrahydrofolate
binding site structure, overview
Candidatus Pelagibacter ubique
Cloned(Commentary) (protein specific)
Commentary
Organism
gene dmdA, expression in Escherichia coli
Candidatus Pelagibacter ubique
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
tetrahydrofolate
binding site structure, overview
Candidatus Pelagibacter ubique
Crystallization (Commentary) (protein specific)
Crystallization
Organism
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
Candidatus Pelagibacter ubique
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
Candidatus Pelagibacter ubique
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
2-(dimethylsulfonio)propanoate + tetrahydrofolate
Candidatus Pelagibacter ubique
-
2-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant DmdA from Escherichia coli
Candidatus Pelagibacter ubique
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2-(dimethylsulfonio)propanoate + tetrahydrofolate
-
720998
Candidatus Pelagibacter ubique
2-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate
-
-
-
?
2-(dimethylsulfonio)propanoate + tetrahydrofolate
DmdA catalyzes a redox-neutral methyl transfer reaction to produce 5-methyltetrahydrofolate
720998
Candidatus Pelagibacter ubique
2-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
More
structure of apoenzyme DmdA and domain architecture, overview
Candidatus Pelagibacter ubique
General Information
General Information
Commentary
Organism
evolution
DmdA belongs to a diverse family of enzymes, the overall fold of the DmdA is not similar to other enzymes that typically utilize the reduced form of tetrahydrofolate and in fact is a triple domain structure similar to what has been observed for the glycine cleavage T protein or sarcosine oxidase. All other THF binding fold enzymes produce 5,10-methylene-tetrahydrofolate. The relative positioning of Y206 in DmdA is different in comparison to the other THF dependent enzymes
Candidatus Pelagibacter ubique
General Information (protein specific)
General Information
Commentary
Organism
evolution
DmdA belongs to a diverse family of enzymes, the overall fold of the DmdA is not similar to other enzymes that typically utilize the reduced form of tetrahydrofolate and in fact is a triple domain structure similar to what has been observed for the glycine cleavage T protein or sarcosine oxidase. All other THF binding fold enzymes produce 5,10-methylene-tetrahydrofolate. The relative positioning of Y206 in DmdA is different in comparison to the other THF dependent enzymes
Candidatus Pelagibacter ubique
Other publictions for EC 2.1.1.269
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
735504
Cui
Abundance and distribution of ...
Candidatus Pelagibacter ubique, Candidatus Pelagibacter ubique HTCC7211, Candidatus Puniceispirillum marinum, Candidatus Puniceispirillum marinum IMCC1322, Roseobacter sp.
Appl. Environ. Microbiol.
81
4184-4194
2015
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3
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9
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3
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6
6
-
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-
736286
Varaljay
Single-taxon field measurement ...
Roseobacter sp., Roseobacter sp. HTCC 2255, Ruegeria pomeroyi
ISME J.
9
1677-1686
2015
-
-
2
-
-
-
-
-
-
-
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-
-
3
-
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2
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4
4
-
-
-
720998
Schuller
Structures of dimethylsulfonio ...
Candidatus Pelagibacter ubique, Candidatus Pelagibacter ubique HTCC1062
Protein Sci.
21
289-298
2012
-
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1
1
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1
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6
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1
1
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2
1
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1
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1
1
2
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1
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1
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2
1
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1
1
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718639
Howard
Changes in dimethylsulfoniopro ...
Candidatus Pelagibacter ubique, Candidatus Pelagibacter ubique HTCC7211, Candidatus Puniceispirillum marinum, Flavobacteriaceae, Rhodobacterales, Rhodospirillales, Roseobacter sp., Sphingomonadales, unidentified marine bacterioplankton, unidentified marine bacterioplankton HTCC2080
Appl. Environ. Microbiol.
77
524-531
2011
-
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4
-
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-
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15
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4
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8
8
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-
698600
Reisch
Dimethylsulfoniopropionate-dep ...
Candidatus Pelagibacter ubique, Candidatus Pelagibacter ubique HTCC1062, Ruegeria pomeroyi
J. Bacteriol.
190
8018-8024
2008
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2
-
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8
7
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4
-
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12
-
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2
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12
2
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4
2
2
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2
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2
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8
2
7
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5
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3
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-
12
3
-
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4
3
3
-
-
-
-
-
-
2
2
701221
Howard
Bacterial taxa that limit sulf ...
Candidatus Pelagibacter ubique, Ruegeria pomeroyi DSS-3
Science
314
649-652
2006
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1
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4
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4
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721447
Jansen
Tetrahydrofolate serves as a m ...
uncultured bacterium, uncultured bacterium WN
Arch. Microbiol.
169
84-87
1998
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2
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2
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1
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1
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4
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1
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1
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