Sandbox Reserved 497: Difference between revisions
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==Mechanism of Action== | ==Mechanism of Action== | ||
A proposed mechanism for the methyl transfer reaction catalyzed by DmdA has recently been published based on the known structural characteristics of DmdA as well as | A proposed mechanism for the methyl transfer reaction catalyzed by DmdA has recently been published based on the known structural characteristics of DmdA as well as the known characteristics of other reactions, namely redox-neutral methyl transfer reactions involving THF as well as reactions that involve a methyl transfer from a sulfonium atom to a nitrogen atom | ||
<ref> Schuller, D.J., Reisch, C.R., Moran, M.A., Whitman, W.B., Lanzilotta, W.N. (2012) Structures of dimethylsulfoniopropinate-dependent demethylase from the marine organism pelagabacter ubique. Protein Sci. 21: 289-298. </ref>. This proposed mechanism is very similar to the mechanism for S-adenosylmethionine (SAM)-dependent N-methyltransferases. In particular, the proposed mechanism for the methyl transfer reaction catalyzed by DmdA involves an SN2 intermediate with a concerted methyl group and a proton transfer mediated by a water molecule present in the active site. This proposed reaction is logical due to the location of the active site, which is highly acessible by water, as well as the <scene name='Sandbox_Reserved_497/Acidicactivesite/1'>acidic side chains </scene> present in the active site. Research suggests that the presence of hydrogen bonds involving acidic residues polarizes the substrate thus lowering the enrgy barrier of the reaction and facilitating the mechanism for (SAM)-dependent N-methyltransferases and the homologous proposed mechanism for the DmdA enzymatic reaction. Further support for the proposed mechanism for the reaction catalyzed by DmdA is provided by the presence of a sulfonium atom in DMSP, the substrate for DmdA, as the presence of this atom tends to make methyl a good leaving group. Finally this proposed mechanism is also supported by the presence of specific structurally significant amino acids in DmdA, some of which were discussed above, as they facilitate hydrogen bonding, ring stacking, and other key interactions that make DmdA structurally homologous to related proteins GcvT family but enzymatically homologous to (SAM)-dependent N-methyltransferases. | <ref> Schuller, D.J., Reisch, C.R., Moran, M.A., Whitman, W.B., Lanzilotta, W.N. (2012) Structures of dimethylsulfoniopropinate-dependent demethylase from the marine organism pelagabacter ubique. Protein Sci. 21: 289-298. </ref>. This proposed mechanism is very similar to the mechanism for S-adenosylmethionine (SAM)-dependent N-methyltransferases. In particular, the proposed mechanism for the methyl transfer reaction catalyzed by DmdA involves an SN2 intermediate with a concerted methyl group and a proton transfer mediated by a water molecule present in the active site. This proposed reaction is logical due to the location of the active site, which is highly acessible by water, as well as the <scene name='Sandbox_Reserved_497/Acidicactivesite/1'>acidic side chains </scene> present in the active site. Research suggests that the presence of hydrogen bonds involving acidic residues polarizes the substrate thus lowering the enrgy barrier of the reaction and facilitating the mechanism for (SAM)-dependent N-methyltransferases and the homologous proposed mechanism for the DmdA enzymatic reaction. Further support for the proposed mechanism for the reaction catalyzed by DmdA is provided by the presence of a sulfonium atom in DMSP, the substrate for DmdA, as the presence of this atom tends to make methyl a good leaving group. Finally this proposed mechanism is also supported by the presence of specific structurally significant amino acids in DmdA, some of which were discussed above, as they facilitate hydrogen bonding, ring stacking, and other key interactions that make DmdA structurally homologous to related proteins GcvT family but enzymatically homologous to (SAM)-dependent N-methyltransferases. | ||