Proteopedia - User contributions [en]

User:Kara Tinker

2013-04-29T19:10:03Z

Kara Tinker:

[[Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)]]

Aminomethyltransferase

2012-09-18T14:49:26Z

Kara Tinker:

=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) complex with glycerol and sodium ion, [[3tfh]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). '''Dimethylsulfoniopropionate-Dependent Demethylase''' (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified '''dimethylsulfoniopropionate-dependendent demethylase''' (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|250px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al. and is reproduced with permission of John Wiley & Sons, Inc.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|550px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al. and is reproduced with permission of John Wiley & Sons, Inc.]]

==Possible Applications==

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/>

Sandbox Reserved 497

2012-07-10T02:29:58Z

Kara Tinker:

Please do not delete this page until after 01/8/2012. It is currently in the process of being published.


{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|250px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|550px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

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/>

User:Kara Tinker

2012-07-10T02:17:28Z

Kara Tinker:

My name is Kara Tinker. I am a senior in biochemistry and microbiology at North Carolina State University. This institution is located in Raleigh, North Carolina, USA. After graduating with my bachelor's degree, I plan to attend the University of Georgia in order to work on my graduate degree in microbiology.

[[Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)]]

Sandbox Reserved 497

2012-06-01T14:14:55Z

Kara Tinker:

Please do not delete this page until after 01/7/2012. It is currently in the process of being published.


{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|250px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|550px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

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/>

Aminomethyltransferase

2012-06-01T02:56:33Z

Kara Tinker: New page: =Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)= <Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3...

=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|250px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|550px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

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/>

Sandbox Reserved 497

2012-05-03T02:22:45Z

Kara Tinker: /* Possible Applications */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|250px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|550px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

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/>

Sandbox Reserved 497

2012-05-03T02:22:16Z

Kara Tinker: /* Possible Applications */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|250px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|550px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

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 amoung a wide range of diverse taxa.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T02:21:16Z

Kara Tinker: /* Possible Applications */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|250px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|550px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

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 amoung a wide range of diverse taxa.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T02:20:18Z

Kara Tinker: /* Possible Applications */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|250px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|550px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

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 options 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 amoung a wide range of diverse taxa.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T02:20:03Z

Kara Tinker: /* Possible Applications */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|250px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|550px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

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 options 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 amoung a wide range of diverse taxa.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T02:17:25Z

Kara Tinker: /* Possible Applications */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|250px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|550px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

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 options can even begin to be considered. Currently, experiments are being conducted in order to identify and characterize DMSP-degrading organisms. 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 this analysis suggests that a significant percentage of marine bacteria are involved in DMSP demethylation as the gene to produce DmdA has been found amoung a wide range of diverse taxa. Similarly, experiments are also being conducted in order to identify the role of DmdA in certain environmental conditions, such as 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>.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T02:15:11Z

Kara Tinker: /* Possible Applications */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|250px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|550px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

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 options can be considered. Experiments have been conducted in order identify and characterize DMSP-degrading organisms. 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 experiments suggest that a significant percentage of marine bacteria are involved in DMSP demethylation as the gene to produce DmdA has been found amoung a wide range of diverse taxa. Similarly, experiments are also being conducted in order to identify the role of DmdA in certain environmental conditions, such as 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>.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T02:14:41Z

Kara Tinker: /* Possible Applications */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|250px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|550px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

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 options can be considered. Currently research is being conducted in order identify and characterize DMSP-degrading organisms. 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 experiments suggest that a significant percentage of marine bacteria are involved in DMSP demethylation as the gene to produce DmdA has been found amoung a wide range of diverse taxa. Similarly, experiments are also being conducted in order to identify the role of DmdA in certain environmental conditions, such as 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>.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T02:13:06Z

Kara Tinker: /* Possible Applications */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|250px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|550px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

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 options can be considered. Currently experiments are being conducted in order identify and characterize DMSP-degrading organisms. 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>. As of now, it currently appears that a significant percentage of marine bacteria are involved in DMSP demethylation as the gene to produce DmdA has been found amoung a wide range of diverse taxa.Similarly, experiments are also being conducted in order to identify the role of DmdA in certain environmental conditions, such as 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>.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T02:09:44Z

Kara Tinker: /* Possible Applications */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|250px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|550px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

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 options can be considered. Currently experiments are being conducted in order identify and characterize DMSP-degrading organisms. 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>. Similarly, experiments are also being conducted in order to identify the role of DmdA in certain environmental conditions, such as 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>.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T02:08:50Z

Kara Tinker: /* Possible Applications */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|250px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|550px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

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 options can be considered. Currently experiments are being conducted in order identify and characterize DMSP-degrading organisms. 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>. Similarly, experiments are also being conducted in order to the role of DmdA in certain environmental conditions, such as 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>.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T02:08:16Z

Kara Tinker: /* Possible Applications */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|250px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|550px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

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 be have significant biogeochemical and bioremediation applications. However, there is a significant amount of research that must be conducted before those options can be considered. Currently experiments are being conducted in order identify and characterize DMSP-degrading organisms. 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>. Similarly, experiments are also being conducted in order to the role of DmdA in certain environmental conditions, such as 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>.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T02:07:24Z

Kara Tinker: /* Possible Applications */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|250px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|550px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

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 be useful in biogeochemical or bioremediation applications. However, there is a significant amount of research that must be conducted before those options can be considered. Currently experiments are being conducted in order identify and characterize DMSP-degrading organisms. 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>. Similarly, experiments are also being conducted in order to the role of DmdA in certain environmental conditions, such as 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>.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T02:06:58Z

Kara Tinker: /* Possible Applications */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|250px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|550px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

DMSP and its degradation products, particularly dimethyl sulfide (DMS), play a key role in the sulfur cycle. Therefore a complete understanding of the 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 be useful in biogeochemical or bioremediation applications. However, there is a significant amount of research that must be conducted before those options can be considered. Currently experiments are being conducted in order identify and characterize DMSP-degrading organisms. 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>. Similarly, experiments are also being conducted in order to the role of DmdA in certain environmental conditions, such as 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>.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T01:35:57Z

Kara Tinker: /* Possible Applications */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|250px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|550px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

DMSP and its degradation products, particularly dimethyl sulfide (DMS), play a key role in the sulfur cycle. Therefore a complete understanding of the both the cleavage and demethylation pathways as well as the enzymes involved could have significant environmental implications.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T01:28:49Z

Kara Tinker: /* Possible Applications */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|250px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|550px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

DMSP and its degradation products, particular DMS, play a key role in the sulfur cycle. Therefore a complete understanding of the demethylation pathway and the enzymes involved could have significant environmental implications.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T01:24:09Z

Kara Tinker: /* Possible Applications */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|250px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|550px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

DMSP is a key

DmdA is the enzyme responsible for the initial step in the demethylation pathway of DMSP.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T00:21:04Z

Kara Tinker: /* Mechanism of Action */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|250px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|550px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

DmdA is the enzyme responsible for the initial step in the demethylation pathway of DMSP.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T00:20:41Z

Kara Tinker: /* Structure */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|250px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|500px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

DmdA is the enzyme responsible for the initial step in the demethylation pathway of DMSP.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T00:20:21Z

Kara Tinker: /* Mechanism of Action */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|225px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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|500px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

DmdA is the enzyme responsible for the initial step in the demethylation pathway of DMSP.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T00:19:18Z

Kara Tinker: /* Mechanism of Action */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|225px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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 GcvT family but enzymatically homologous to (SAM)-dependent N-methyltransferases.

[[Image:DmdA_Mechanism.jpg|thumb|500px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

DmdA is the enzyme responsible for the initial step in the demethylation pathway of DMSP.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T00:18:35Z

Kara Tinker: /* Mechanism of Action */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|225px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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 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 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 GcvT family but enzymatically homologous to (SAM)-dependent N-methyltransferases.

[[Image:DmdA_Mechanism.jpg|thumb|500px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

DmdA is the enzyme responsible for the initial step in the demethylation pathway of DMSP.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T00:16:57Z

Kara Tinker: /* Mechanism of Action */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|225px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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 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.

[[Image:DmdA_Mechanism.jpg|thumb|500px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

DmdA is the enzyme responsible for the initial step in the demethylation pathway of DMSP.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T00:16:08Z

Kara Tinker: /* Mechanism of Action */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|225px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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 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 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.

[[Image:DmdA_Mechanism.jpg|thumb|500px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

DmdA is the enzyme responsible for the initial step in the demethylation pathway of DMSP.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T00:15:06Z

Kara Tinker: /* Mechanism of Action */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|225px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 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.

[[Image:DmdA_Mechanism.jpg|thumb|500px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

DmdA is the enzyme responsible for the initial step in the demethylation pathway of DMSP.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T00:14:18Z

Kara Tinker: /* Mechanism of Action */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|225px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 what is known about 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.

[[Image:DmdA_Mechanism.jpg|thumb|500px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

DmdA is the enzyme responsible for the initial step in the demethylation pathway of DMSP.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T00:12:39Z

Kara Tinker: /* Mechanism of Action */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|225px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 what is known about other reactions, namely redox-neutral methyl transfer reactions involving THF as well 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, as well as the reasoning behind it, 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, since the presence of this atom tends to make methyl a fairly 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.

[[Image:DmdA_Mechanism.jpg|thumb|500px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

DmdA is the enzyme responsible for the initial step in the demethylation pathway of DMSP.

==References==

<references/>

Sandbox Reserved 497

2012-05-03T00:11:16Z

Kara Tinker: /* Mechanism of Action */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|225px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 what is known about other reactions, namely redox-neutral methyl transfer reactions involving THF as well 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, as well as the reasoning behind it, 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, since the presence of this atom tends to make methyl a fairly 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 similar to other proteins GcvT family but enzymatic ally similar to (SAM)-dependent N-methyltransferases.

[[Image:DmdA_Mechanism.jpg|thumb|500px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

DmdA is the enzyme responsible for the initial step in the demethylation pathway of DMSP.

==References==

<references/>

Sandbox Reserved 497

2012-05-02T23:57:11Z

Kara Tinker: /* Mechanism of Action */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|225px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 what is known about similar reactions, namely redox-neutral methyl transfer reactions involving THF as well 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, as well as the reasoning behind it, 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. 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 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 fairly good leaving group.

[[Image:DmdA_Mechanism.jpg|thumb|500px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

DmdA is the enzyme responsible for the initial step in the demethylation pathway of DMSP.

==References==

<references/>

Sandbox Reserved 497

2012-05-02T23:51:26Z

Kara Tinker: /* Mechanism of Action */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|225px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 what is known about similar reactions, namely redox-neutral methyl transfer reactions involving THF as well 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, as well as the reasoning behind it, 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. This 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. In addition, the proposed mechanism is also reasonable because the substrate for DmdA, DMSP, contains a sulfonium atom which tends to make methyl a fairly good leaving group.

[[Image:DmdA_Mechanism.jpg|thumb|500px|right|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

==Possible Applications==

DmdA is the enzyme responsible for the initial step in the demethylation pathway of DMSP.

==References==

<references/>

Sandbox Reserved 497

2012-05-02T21:54:37Z

Kara Tinker: /* Structure */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|225px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site cleft is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 what is known about similar reactions, namely redox-neutral methyl transfer reactions involving THF as well 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>. The proposed mechanism involves an SN2 intermediate with a concerted methyl group and a proton transfer mediated by a water molecule present in the active site.

[[Image:DmdA_Mechanism.jpg|thumb|500px|center|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

This proposed reaction seems likely 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. Additionally the substrate for DmdA, DMSP, contains a sulfonium atom which tends to make methyl a fairly good leaving group.

S-adenosylmethionine (SAM)-dependent N-methyltransferases
The proposed mechanism for this reaction

Further support for this proposal comes
from the observation that a number of SAM-dependent
methyltransferases, such as protein arginine,
glycine-N, and phenylethanolamine-N methyltransferase
also help facilitate such a mechanism through
hydrogen bonds involving acidic residues,30,32,33 and
polarization of the nitrogen atom targeted for methyl
transfer. It has been proposed that polarization of
the substrate lowers the energy barrier to the SN2-
like methyl transfer reaction.34,35

==Possible Applications==

DmdA is the enzyme responsible for the initial step in the demethylation pathway of DMSP.

==References==

<references/>

Sandbox Reserved 497

2012-05-02T21:53:59Z

Kara Tinker: /* Structure */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|225px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein, though the active site is highly accessible by water. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 what is known about similar reactions, namely redox-neutral methyl transfer reactions involving THF as well 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>. The proposed mechanism involves an SN2 intermediate with a concerted methyl group and a proton transfer mediated by a water molecule present in the active site.

[[Image:DmdA_Mechanism.jpg|thumb|500px|center|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

This proposed reaction seems likely 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. Additionally the substrate for DmdA, DMSP, contains a sulfonium atom which tends to make methyl a fairly good leaving group.

S-adenosylmethionine (SAM)-dependent N-methyltransferases
The proposed mechanism for this reaction

Further support for this proposal comes
from the observation that a number of SAM-dependent
methyltransferases, such as protein arginine,
glycine-N, and phenylethanolamine-N methyltransferase
also help facilitate such a mechanism through
hydrogen bonds involving acidic residues,30,32,33 and
polarization of the nitrogen atom targeted for methyl
transfer. It has been proposed that polarization of
the substrate lowers the energy barrier to the SN2-
like methyl transfer reaction.34,35

==Possible Applications==

DmdA is the enzyme responsible for the initial step in the demethylation pathway of DMSP.

==References==

<references/>

Sandbox Reserved 497

2012-05-02T21:51:29Z

Kara Tinker: /* Mechanism of Action */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|225px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 what is known about similar reactions, namely redox-neutral methyl transfer reactions involving THF as well 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>. The proposed mechanism involves an SN2 intermediate with a concerted methyl group and a proton transfer mediated by a water molecule present in the active site.

[[Image:DmdA_Mechanism.jpg|thumb|500px|center|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

This proposed reaction seems likely 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. Additionally the substrate for DmdA, DMSP, contains a sulfonium atom which tends to make methyl a fairly good leaving group.

S-adenosylmethionine (SAM)-dependent N-methyltransferases
The proposed mechanism for this reaction

Further support for this proposal comes
from the observation that a number of SAM-dependent
methyltransferases, such as protein arginine,
glycine-N, and phenylethanolamine-N methyltransferase
also help facilitate such a mechanism through
hydrogen bonds involving acidic residues,30,32,33 and
polarization of the nitrogen atom targeted for methyl
transfer. It has been proposed that polarization of
the substrate lowers the energy barrier to the SN2-
like methyl transfer reaction.34,35

==Possible Applications==

DmdA is the enzyme responsible for the initial step in the demethylation pathway of DMSP.

==References==

<references/>

Sandbox Reserved 497

2012-05-02T21:50:50Z

Kara Tinker: /* Mechanism of Action */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|225px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 what is known about similar reactions, namely redox-neutral methyl transfer reactions involving THF as well 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>. The proposed mechanism involves an SN2 intermediate with a concerted methyl group and a proton transfer mediated by a water molecule present in the active site.

[[Image:DmdA_Mechanism.jpg|thumb|550px|center|The proposed mechanism for the methyl transfer reaction catalyzed by DmdA. This image was obtained directly from Schuller et al.]]

This proposed reaction seems likely 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. Additionally the substrate for DmdA, DMSP, contains a sulfonium atom which tends to make methyl a fairly good leaving group.

S-adenosylmethionine (SAM)-dependent N-methyltransferases
The proposed mechanism for this reaction

Further support for this proposal comes
from the observation that a number of SAM-dependent
methyltransferases, such as protein arginine,
glycine-N, and phenylethanolamine-N methyltransferase
also help facilitate such a mechanism through
hydrogen bonds involving acidic residues,30,32,33 and
polarization of the nitrogen atom targeted for methyl
transfer. It has been proposed that polarization of
the substrate lowers the energy barrier to the SN2-
like methyl transfer reaction.34,35

==Possible Applications==

DmdA is the enzyme responsible for the initial step in the demethylation pathway of DMSP.

==References==

<references/>

Sandbox Reserved 497

2012-05-02T21:49:31Z

Kara Tinker: /* Mechanism of Action */

{{Sandbox_Reserved_Robert_B_Rose_1}}


=Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)=
<Structure load='3TFH' size='400' frame='true' align='right' caption='Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), [[3TFH]]' scene='Insert optional scene name here' />

==Introduction==

Dimethylsulfoniproprionate (DMSP) is a common metabolite produced by marine microorganisms and it acts as a significant carbon and sulfur source for marine bacteria. Degradation of DMSP occurs by either the cleavage pathway or the demethylation pathway <ref> Reisch, C.R., Moran, M.A., Whitman, W.B. (2008). Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190: 8018-8024. </ref>. Understanding both of these degradation pathways is essential due to the key role of DMSP and its degradation product, dimethylsulfide (DMS), in the environmental sulfur cycle <ref>Malin, G. (2006). New Pieces for the Marine Sulfur Cycle Jigsaw. Science. 314: 607-608.</ref>. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Recent research has identified dimethylsulfoniopropionate-dependendent demethylase (DmdA) as the inital enzyme in the demethylation pathway. DmdA facilitates the conversion of DMSP into MMPA by acting as a methyl transferase.
Because DmdA has only recently been isolated and characterized, there is still much that is unknown about the properties of DmdA. A proposed reaction mechanism for demethylation of DmdA has recently been published. Additionally, it is known that tetrahydrofolate (THF) is a cofactor in this enzymatic reaction and the key amino acids responsible for the binding of DMSP and THF to DmdA are in the process of being identified.

==Structure==

[[Image:Domains+ActiveSite.jpg|thumb|225px|left|Panel A is an image of the protein dimer DmdA. Panel B contains the three labeled domains and the active cleft site of DmdA. This image was obtained directly from Schuller et al.]]

The structure of DmdA has recently been solved through the use of X-Ray diffraction <ref> Image from the RCSB PDB (www.pdb.org) of PDB ID 3TFH (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>. The structure is a protein dimer composed of 369 amino acid residues and contains three distinct domains and four <scene name='Sandbox_Reserved_497/Ligand/1'>ligands</scene>, two of which are sodium ions and two of which are glycerol. The structure is composed of both <scene name='Sandbox_Reserved_497/Helix/1'>alpha-helices</scene> and <scene name='Sandbox_Reserved_497/Sheets/1'>beta-sheets</scene> and has <scene name='Sandbox_Reserved_497/Hydrophobic/1'>hydrophobic</scene> regions dispersed throughout the protein. The active site cleft is located between domain 1 and domain 2. Each domain contains unique identifying structural components. <scene name='Sandbox_Reserved_497/Domain1/1'>Domain 1</scene> is characterized by a Greek Key surrounded by three alpha-helices while <scene name='Sandbox_Reserved_497/Domain2/1'>domain 2</scene> contains a five-stranded antiparallel beta-sheet with alpha-helices on either side. Alternatively, <scene name='Sandbox_Reserved_497/Domain3/1'>domain 3</scene> has a distorted jellyroll formation. While DmdA belongs to the glycine cleavage T-protein (GcvT) family there is only approximately <scene name='Sandbox_Reserved_497/Conserved/1'>25% sequence identity</scene>. These few conserved amino acids likely interact with THF, which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. While the exact binding mechanism of THF to the active site cleft of DmdA is still unknown, it appears as if the mechanism is unlike the general mechanism used by enzymes in the GcvT family and is unique to DmdA. In particular, amino acid residues <scene name='Sandbox_Reserved_497/Thf/1'>95, 177, 178, 204, and 206</scene> may be essential for THF binding as they assist in ring stacking as well as have the potential for hydrogen bonding. Similarly, research is still being conducted in order to determine the amino acids essential for the binding of the substrate, DMSP, to DmdA. So far it appears as if amino acid residues <scene name='Sandbox_Reserved_497/Dmsp/1'>11, 32, 197, and 246</scene> are important due to their potential for hydrogen bonding.

==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 what is known about similar reactions, namely redox-neutral methyl transfer reactions involving THF as well 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>. The proposed mechanism 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 seems likely 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. Additionally the substrate for DmdA, DMSP, contains a sulfonium atom which tends to make methyl a fairly good leaving group.

S-adenosylmethionine (SAM)-dependent N-methyltransferases
The proposed mechanism for this reaction

Further support for this proposal comes
from the observation that a number of SAM-dependent
methyltransferases, such as protein arginine,
glycine-N, and phenylethanolamine-N methyltransferase
also help facilitate such a mechanism through
hydrogen bonds involving acidic residues,30,32,33 and
polarization of the nitrogen atom targeted for methyl
transfer. It has been proposed that polarization of
the substrate lowers the energy barrier to the SN2-
like methyl transfer reaction.34,35

[[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==

DmdA is the enzyme responsible for the initial step in the demethylation pathway of DMSP.

==References==

<references/>

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2012-05-02T21:42:29Z

Kara Tinker: /* Mechanism of Action */

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Kara Tinker: /* Mechanism of Action */

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2012-05-02T21:41:06Z

Kara Tinker: /* Mechanism of Action */

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2012-05-02T21:40:48Z

Kara Tinker: /* Possible Applications */

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2012-05-02T21:38:34Z

Kara Tinker: /* Mechanism of Action */

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2012-05-02T21:38:12Z

Kara Tinker: /* Mechanism of Action */

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2012-05-02T21:30:21Z

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2012-05-02T21:14:59Z

Kara Tinker: /* Structure */

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Kara Tinker: /* Mechanism of Action */