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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. One end of Oleic Acid has a carboxylic acid which has a hydrogen bond with and a water molecule. The Oleic Acid chain of carbons is surrounded by non-polar amino acids such as valine.
Structural highlights
This enzyme is a , chains A and B are two asymmetrical monomers that contain both . 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 of the protein shows the ligand covered by the enzyme with the polar end sticking out of the cavity.
