Sandbox Reserved 497: Difference between revisions
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==Structure== | ==Structure== | ||
[[Image:Domains+ActiveSite.jpg|thumb|225px|left| | [[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. Image 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 tetrahydrofolate (THF), which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. | 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 tetrahydrofolate (THF), which is a cofactor required by DmdA as well as many other enzymes in the GcvT family. | ||
