Jake Ezell Sandbox 2: Difference between revisions
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==Malate Dehydrogenase== | ==Malate Dehydrogenase== | ||
Malate Dehydrogenase (MDH)(PDB entry [http://www.pdb.org/pdb/explore/explore.do?structureId=2X0I 2x0i]) is most known for its role in the metabolic pathway in the tricarboxylic acid cycle[http://en.wikipedia.org/wiki/Citric_acid_cycle]; however, the enzyme is also in many other metabolic pathways such as glyoxylate bypass, amino acid synthesis, glucogenesis, and oxidation/reduction balance <ref>PMID:12537350</ref>. It is classified as a oxidoreductase[http://en.wikipedia.org/wiki/Oxidoreductase]. Malate Dehydrogenase has been extensively studied due to its many isozymes<ref>PMID:20173310</ref>. The enzyme exists in two places inside a cell, in the mitochondria and cytoplasm. In the mitochondria, the enzyme catalyzes the reaction of malate to oxaloacetate; but in the cytoplasm, the enzyme catalyzes oxaloacetate to malate to allow transport <ref>PMID:20173310</ref>. This conversion is an essential catalytic step in each different metabolic mechanism. The enzyme malate dehydrogenase is composed of either a dimer or tetramer <ref>PMID: 9834842<ref/>. During catalysis, the enzyme subunits are non-cooperative between active sites. The mitochondrial MDH is allosterically controlled by citrate, but no other known metabolic regulation mechanisms have been discovered. | Malate Dehydrogenase (MDH)(PDB entry [http://www.pdb.org/pdb/explore/explore.do?structureId=2X0I 2x0i]) is most known for its role in the metabolic pathway in the tricarboxylic acid cycle[http://en.wikipedia.org/wiki/Citric_acid_cycle]; however, the enzyme is also in many other metabolic pathways such as glyoxylate bypass, amino acid synthesis, glucogenesis, and oxidation/reduction balance <ref>PMID:12537350</ref> . It is classified as a oxidoreductase[http://en.wikipedia.org/wiki/Oxidoreductase]. Malate Dehydrogenase has been extensively studied due to its many isozymes <ref>PMID:20173310</ref>. The enzyme exists in two places inside a cell, in the mitochondria and cytoplasm. In the mitochondria, the enzyme catalyzes the reaction of malate to oxaloacetate; but in the cytoplasm, the enzyme catalyzes oxaloacetate to malate to allow transport <ref>PMID:20173310</ref> . This conversion is an essential catalytic step in each different metabolic mechanism. The enzyme malate dehydrogenase is composed of either a dimer or tetramer <ref>PMID: 9834842<ref/> . During catalysis, the enzyme subunits are non-cooperative between active sites. The mitochondrial MDH is allosterically controlled by citrate, but no other known metabolic regulation mechanisms have been discovered. | ||
The secondary structure of a single subunit contains a <scene name='Malate_dehydrogenase/Beta_sheeting_backbone/1'>9 beta sheet parallel backbone</scene> wrapped by <scene name='Malate_dehydrogenase/Alpha_wrapping_betas/1'>9 large alpha helices</scene>. Near the sodium bound end, 4 small anti-parallel beta sheets and 1 small alpha helix enable a turn in the residue chain<scene name='Malate_dehydrogenase/Small_turn/1'>(small turn)</scene>. Opposite the sodium bound ligand, 6 alpha helices point towards a common point, three on each side of the beta sheet backbone. The alpha helices form a <scene name='Jake_Ezell_Sandbox_2/Small_groove_nad/1'>small groove</scene> for a NAD+ cofactor to attach near the beta sheeting. The structure most nearly resembles an alternating alpha/beta classification. As for the 3D structure, the enzyme forms a sort of | The secondary structure of a single subunit contains a <scene name='Malate_dehydrogenase/Beta_sheeting_backbone/1'>9 beta sheet parallel backbone</scene> wrapped by <scene name='Malate_dehydrogenase/Alpha_wrapping_betas/1'>9 large alpha helices</scene>. Near the sodium bound end, 4 small anti-parallel beta sheets and 1 small alpha helix enable a turn in the residue chain<scene name='Malate_dehydrogenase/Small_turn/1'>(small turn)</scene>. Opposite the sodium bound ligand, 6 alpha helices point towards a common point, three on each side of the beta sheet backbone. The alpha helices form a <scene name='Jake_Ezell_Sandbox_2/Small_groove_nad/1'>small groove</scene> for a NAD+ cofactor to attach near the beta sheeting. The structure most nearly resembles an alternating alpha/beta classification. As for the 3D structure, the enzyme forms a sort of | ||