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Please do not delete this page until after 01/8/2012. It is currently in the process of being published. | |||
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<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 cleft, 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 energy barrier of the reaction and facilitating the mechanism for (SAM)-dependent N-methyltransferases and the nearly identical proposed mechanism for the DmdA enzymatic reaction. Further support for this proposed mechanism is provided by the presence of a sulfonium atom in DMSP, the substrate for DmdA, as the presence of this atom tends to increase the likelihood of methyl acting as a 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 in the 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 cleft, 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 energy barrier of the reaction and facilitating the mechanism for (SAM)-dependent N-methyltransferases and the nearly identical proposed mechanism for the DmdA enzymatic reaction. Further support for this proposed mechanism is provided by the presence of a sulfonium atom in DMSP, the substrate for DmdA, as the presence of this atom tends to increase the likelihood of methyl acting as a 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 in the GcvT family but enzymatically homologous to (SAM)-dependent N-methyltransferases. | ||
[[Image:DmdA_Mechanism.jpg|thumb| | [[Image:DmdA_Mechanism.jpg|thumb|550px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]] | ||
==Possible Applications== | ==Possible Applications== | ||
DmdA is the | DMSP and its degradation products, particularly dimethyl sulfide (DMS), play a key role in the sulfur cycle. Therefore a complete understanding of both the cleavage and demethylation pathways as well as the enzymes involved could have significant environmental implications. In particular, it currently appears that certain types of organisms such as ''Pelagabacter ubique,'' the microbe that DmdA was originally isolated from, utilize the demethylation pathway over the cleavage pathway because it provides an additional carbon energy source. The ability to not only identify the organisms that degrade DMSP, but also the conditions under which each pathway is more favorable, could have significant biogeochemical and bioremediation applications. However, there is a significant amount of research that must be conducted before those applications can even begin to be considered. Current research is focused on identifying and characterizing DMSP-degrading organisms as well as the role of DmdA in certain environmental conditions, such an induced phytoplankton bloom<ref>Howard, E.C., Sun, S., Reisch, C.R., del Valle, D.A>, Burgmann, H., Kiene, R.P., and Moran, M.A. (2011). Changes in dimethylsuloniopropionate demethylase gene assemblages in response to an induced phytoplankton bloom. Appl Environ Microbiol. 77(2):524-531.</ref>. For example, oceanic metagenomic data has been collected and analyzed in order to determine what marine microorganisms contain the gene to produce DmdA <ref>Howard, E.C., Sun, S., Biers, E.J., and Moran, M.A. (2008). Abundant and diverse bacteria involved in DMSP degradation in marine surface waters. Environ Microbiol. 10(9);2397-2410.</ref>. The results of these analysis suggest that a significant percentage of marine bacteria are involved in DMSP demethylation, as the gene to produce DmdA has been found among a wide range of diverse taxa. | ||
==References== | ==References== | ||
<references/> | <references/> | ||