Sandbox Reserved 497: Difference between revisions

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 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.