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Literature summary extracted from

  • Schuller, D.J.; Reisch, C.R.; Moran, M.A.; Whitman, W.B.; Lanzilotta, W.N.
    Structures of dimethylsulfoniopropionate-dependent demethylase from the marine organism Pelagabacter ubique (2012), Protein Sci., 21, 289-298.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.1.1.269 gene dmdA, expression in Escherichia coli Candidatus Pelagibacter ubique

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
2.1.1.269 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
2.1.1.269 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)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.1.1.269 2-(dimethylsulfonio)propanoate + tetrahydrofolate Candidatus Pelagibacter ubique
-
 2-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.1.1.269 Candidatus Pelagibacter ubique
-
 gene dmda or SAR11_0246
-
2.1.1.269 Candidatus Pelagibacter ubique Q4FP21
-
-
2.1.1.269 Candidatus Pelagibacter ubique HTCC1062 Q4FP21
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
2.1.1.269 recombinant DmdA from Escherichia coli Candidatus Pelagibacter ubique

Reaction

EC Number Reaction Comment Organism Reaction ID
2.1.1.269 S,S-dimethyl-beta-propiothetin + tetrahydrofolate = 3-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate DmdA catalyzes a redox-neutral methyl transfer reaction to produce 5-methyltetrahydrofolate, mechanism, overview Candidatus Pelagibacter ubique
a
2.1.1.269 S,S-dimethyl-beta-propiothetin + tetrahydrofolate = 3-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate concerted mechanism in which methyl transfer is coupled to proton transfer Candidatus Pelagibacter ubique
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.1.1.269 2-(dimethylsulfonio)propanoate + tetrahydrofolate
-
 Candidatus Pelagibacter ubique 2-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate
-
 ?
2.1.1.269 2-(dimethylsulfonio)propanoate + tetrahydrofolate DmdA catalyzes a redox-neutral methyl transfer reaction to produce 5-methyltetrahydrofolate Candidatus Pelagibacter ubique 2-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate
-
 ?

Subunits

EC Number Subunits Comment Organism
2.1.1.269 More structure of apoenzyme DmdA and domain architecture, overview Candidatus Pelagibacter ubique

Synonyms

EC Number Synonyms Comment Organism
2.1.1.269 dimethylsufoniopropionate-dependent demethylase A
-
 Candidatus Pelagibacter ubique
2.1.1.269 DmdA
-
 Candidatus Pelagibacter ubique

Cofactor

EC Number Cofactor Comment Organism Structure
2.1.1.269 tetrahydrofolate binding site structure, overview Candidatus Pelagibacter ubique

General Information

EC Number General Information Comment Organism
2.1.1.269 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