Sandbox Reserved 497: Difference between revisions

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==Structure==
==Structure==
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 active site cleft is located between domain 1 and domain 2. Each domain contains 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 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 a <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 tetrahydrofolate (THF), which is a cofactor required by DmdA as well as many other enzymes in the GcvT family.


==Mechanism of Action==
==Mechanism of Action==

Revision as of 17:54, 2 May 2012

This Sandbox is Reserved from 13/03/2012, through 01/06/2012 for use in the course "Proteins and Molecular Mechanisms" taught by Robert B. Rose at the North Carolina State University, Raleigh, NC USA. This reservation includes Sandbox Reserved 451 through Sandbox Reserved 500.
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Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)

Dimethylsulfoniopropionate-Dependent Demethylase (DmdA), 3TFH

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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 [1]. The demethylation pathway is characterized by the conversion of DMSP into methylmercaptopropionate (MMPA). Dimethylsulfoniopropionate-Dependendent Demethylase (DmdA) is the first enzyme in the demethylation pathway and facilitates this conversion by acting as a methyl transferase.

Structure

Mechanism of Action

The specific mechanism of DmdA is still being investigated. However, a mechanism was recently proposed [2]

Proposed mechanism

Possible Applications

References

  1. ↑ 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.
  2. ↑ 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.
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