Cloned (Comment) | Organism |
---|---|
gene dmdA, expression in Escherichia coli | Candidatus Pelagibacter ubique |
Crystallization (Comment) | 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 | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
2-(dimethylsulfonio)propanoate + tetrahydrofolate | Candidatus Pelagibacter ubique | - |
2-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate | - |
? |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Candidatus Pelagibacter ubique | - |
gene dmda or SAR11_0246 | - |
Candidatus Pelagibacter ubique | Q4FP21 | - |
- |
Candidatus Pelagibacter ubique HTCC1062 | Q4FP21 | - |
- |
Purification (Comment) | Organism |
---|---|
recombinant DmdA from Escherichia coli | Candidatus Pelagibacter ubique |
Reaction | Comment | Organism | Reaction ID |
---|---|---|---|
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 | |
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 |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
2-(dimethylsulfonio)propanoate + tetrahydrofolate | - |
Candidatus Pelagibacter ubique | 2-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate | - |
? | |
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 | Comment | Organism |
---|---|---|
More | structure of apoenzyme DmdA and domain architecture, overview | Candidatus Pelagibacter ubique |
Synonyms | Comment | Organism |
---|---|---|
dimethylsufoniopropionate-dependent demethylase A | - |
Candidatus Pelagibacter ubique |
DmdA | - |
Candidatus Pelagibacter ubique |
Cofactor | Comment | Organism | Structure |
---|---|---|---|
tetrahydrofolate | binding site structure, overview | Candidatus Pelagibacter ubique |
General Information | Comment | 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 |