Sandbox Reserved 1758
From Proteopedia
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| - | == | + | == Mevalonate 3,5-biphosphate decarboxylase == |
| - | <StructureSection load=' | + | <StructureSection load='7T71' size='340' side='right' caption='7T71' scene=''> |
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs. | This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs. | ||
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue. | You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue. | ||
| - | == Function == | + | == Function of your protein == |
| - | + | ||
| - | == | + | <scene name='93/934002/Cartoon_image/1'>Mevalonate 3,5-biphosphate decarboxylase</scene> 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 <scene name='93/934002/Ligand/2'>ligand</scene> 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 <scene name='93/934002/Asp_281_asp_309/1'>catalytic dyad</scene> is composed of Asp 281 and Asp 309<ref>PMID:35690147</ref>.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 <scene name='93/934002/Ligand/2'>ligand</scene>, such as Oleic Acid, a fatty acid. One end of Oleic Acid has a carboxylic acid which has a hydrogen bond with <scene name='93/934002/Arg_128/1'>Arg 128</scene> and a water molecule. The Oleic Acid chain of carbons is surrounded by non-polar amino acids such as valine. | ||
== Structural highlights == | == Structural highlights == | ||
| - | + | This enzyme is a <scene name='93/934002/Homodimer/1'>homodimer</scene>, chains A and B are two asymmetrical monomers that contain both <scene name='93/934002/Secondary_structure/1'>alpha helices and beta sheets</scene>. 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 <scene name='93/934002/Space-filling_view/1'>space-filling view</scene> of the protein shows the ligand covered by the enzyme with the polar end sticking out of the cavity. | |
| - | This is a | + | |
</StructureSection> | </StructureSection> | ||
== References == | == References == | ||
<references/> | <references/> | ||
Current revision
| This Sandbox is Reserved from November 4, 2022 through January 1, 2023 for use in the course CHEM 351 Biochemistry taught by Bonnie Hall at the Grand View University, Des Moines, USA. This reservation includes Sandbox Reserved 1755 through Sandbox Reserved 1764. |
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Mevalonate 3,5-biphosphate decarboxylase
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References
- ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
- ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
- ↑ Aoki M, Vinokur J, Motoyama K, Ishikawa R, Collazo M, Cascio D, Sawaya MR, Ito T, Bowie JU, Hemmi H. Crystal structure of mevalonate 3,5-bisphosphate decarboxylase reveals insight into the evolution of decarboxylases in the mevalonate metabolic pathways. J Biol Chem. 2022 Jul;298(7):102111. doi: 10.1016/j.jbc.2022.102111. Epub 2022 , Jun 9. PMID:35690147 doi:http://dx.doi.org/10.1016/j.jbc.2022.102111
