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You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

Function of your protein

is found in Picrophilus Torridus, a thermoacidophilic archaeon of the order Thermoplasmatales. The enzyme catalyzes the elimination of the 3-phosphate group from mevalonate 3,5-biphosphate as well as concomitant decarboxylation of the substrate. The protein binds to an amphipathic fatty acid, Oleic Acid. This is the represented in the structure however the authors noted that archaea do not tend to synthesize fatty acids. The authors determined that GGPP or related compounds are possible physiological ligands.

Biological relevance and broader implications

Picrophilus Torridus undergoes Thermoplasma-type MVA (mevalonate) pathway, the enzyme produces ADP in this pathway. This is relevant because the journal is analyzing a distinction between a novel variant of the eukaryotic MVA pathway. When the enzyme binds to a fatty-acid-like structure there is no ATP required for the reaction. There is an evolutionary route from ATP dependent to ATP-independent with the loss of kinase ability.

Important amino acids

The is composed of Asp 281 and Asp 309^[3].The internal surface of the cavity contains hydrophobic amino acid residues. The opening of the cavity holds charged or polar residues including Lys 94, Tyr 99, Arg 128, and Glu 138. This suggests an amphipathic , such as Oleic Acid, a fatty acid. Oleic Acid is an amphipathic fatty acid. One end has a carboxylic acid which has a hydrogen bond with Arg 148 and a water molecule. The Oleic Acid chain of carbons is surrounded by non-polar amino acids such as valine.

Structural highlights

Secondary Structure PtoMBD is a homodimer, chains A and B are two asymmetrical monomers that contain both alpha helices and beta sheets. The chains are nearly identical and contain 12 alpha helices and 12 beta sheets. The outer surface is framed by an antiparallel beta-sheet that is composed of β6, β4,β1, and β12 followed along with the β5 strand. Other antiparallel beta-sheets include the formation of β2, β3, β7, β8 and β9, β11, and β10 strands. These two beta-sheets alongside α1, α8, α9, α10, α11, and α12 helices form the floor of the enzyme as well as a large cleft of the substrate-binding sites. The upper domain of the site is formed of α2, α3, α4, α5, α6, and α7 helices and β5, β6, β4, β1, β12.There is a resemblance to homologous decarboxylases seen in the GHMP kinases superfamily. The PtoMBD homodimer has a calculated mass of 42,186 Da. This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.