Sandbox Reserved 1757

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{{Sandbox_Reserved_BHall_F22}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
{{Sandbox_Reserved_BHall_F22}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
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==Structural Information on Mevalonate 3,5-bisphosphate decarboxylase==
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==Mevalonate 3,5-bisphosphate decarboxylase==
<StructureSection load='7T71' size='340' side='right' caption='Caption for this structure' scene=''>
<StructureSection load='7T71' size='340' side='right' caption='Caption for this structure' scene=''>
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This is a Proteopedia created to explain the function and structure of Mevalonate 3,5-bisphosphate decarboxylase
 
== Function of your protein ==
== Function of your protein ==
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<scene name='93/934001/Rotating_cartoon/1'>Mevalonate 3,5-bisphosphate decarboxylase</scene> is a protein that originates from members of the order Thermoplasmatales, however in this article specifically the Mevalonate 3,5-bisphosphate being studied originated from the species Picrophilus Torridus. The purpose of this protein is to catalyze an elimination reaction in order to remove the 3-phosphate group from mevalonate 3,5-biphosphate and further goes on to decarboxylate the substrate produced thereby removing carboxyl groups from the acidic substrate.
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<scene name='93/934001/Rotating_cartoon/1'>Mevalonate 3,5-bisphosphate decarboxylase</scene> is a protein that originates from members of the order Thermoplasmatales. In this article specifically the Mevalonate 3,5-bisphosphate being studied originated from the species Picrophilus Torridus. The purpose of this protein is to catalyze an elimination reaction in order to remove the 3-phosphate group from mevalonate 3,5-biphosphate and further goes on to decarboxylate the substrate produced thereby removing carboxyl groups from the acidic substrate.
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== Biological relevance and broader implications ==
== Biological relevance and broader implications ==
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This article’s goal was to test the function and relation of the protein Mevalonate 3,5-bisphosphate and compare it to its homologs. The article seeks to explore the evolutionary changes that the protein has gone through that managed to separate it from its suspected evolutionary predecessors which require ATP to function and allowed it to become ATP-independent. This suspected evolutionary relevance is due to the residual signs of the ATP binding site which are still present in the Mevalonate 3,5-bisphosphate despite the protein being completely ATP-independent. This ATP binding site present in Mevalonate 3,5-bisphosphate's likely evolutionary predecessors has been bound to by a ligand similar to a fatty acid.
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[[Image:Oleic Acid.png|300 px|thumb|right|Oleic Acid(suspected ligand present)]]
== Important amino acids==
== Important amino acids==
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The article only really talks about how the ligand, like a fatty acid, lacks an ATP binding site. It also talks about the necessity of the ligand being amphipathic as there are hydrophilic and hydrophobic charges found in the binding site.
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Unfortunately due to the relatively recent studies pertaining to the structure and bind of Mevalonate 3,5-bisphosphate, the researchers are not exactly sure what the ligand present in the protein is. However, through this study, they determined that the closest match they could find for the <scene name='93/934001/Ligand_view/2'>ligand</scene> present is Oleic Acid(OLA). The ligand is bound via hydrogen bonding to H2O and <scene name='93/934001/Arg_128/2'>Arg 128</scene>. Another essential amino acid is the aspartate residue(<scene name='93/934001/Asp_309/1'>Asp309</scene>) as loss of this catalyst results in complete loss of Mevalonate 3,5-bisphosphate decarboxylase activity.
== Structural highlights ==
== Structural highlights ==
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Mevalonate 3,5-bisphosphate is a homodimer made up of <scene name='93/934001/Secondary/1'>40% alpha helices and 60% beta-sheets</scene>. Because Mevalonate 3,5-bisphosphate is a homodimer both molecules present are <scene name='93/934001/Quat/1'>identical</scene> in primary, secondary, and tertiary structure. Mevalonate 3,5-bisphosphate is amphipathic as showcased by the surplus of hydrophobic as well as hydrophilic amino acids present in its <scene name='93/934001/Active_site/2'>Active Site</scene>. This<scene name='93/934001/Active_site/4'> view</scene> also shows us the large cleft for substrate binding present on the molecule.
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The protein is a dimer that contains <scene name='93/934001/Secondary_structure/1'>14 helices and 15 beta sheets</scene> per linked molecule. The ARG 148 forms hydrogen bonds that allow it to pair with Oleic Acid, the protein’s ligand. Protein also requires H2O to be present in order to bind its <scene name='93/934001/Ligand/1'>ligand</scene>. I found it really interesting that the protein only actually attaches to the ligand via small interaction between ARG 148 and water molecules.
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== Other important features ==
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As stated earlier the important amino acids section unfortunately the dimer for Mevalonate 3,5-bisphosphate has not been confirmed but one of the factors that led to the assumption that the unknown ligand is a fatty acid like Oleic Acid was due to the amphipathic nature of the binding site showcased by the presence of non-polar molecules in the binding site as well as polar molecules such as <scene name='93/934001/Binding_site/1'>Lys94, Tyr99, Arg128, and Glu138</scene> surrounding the opening of the cavity.
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This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
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</StructureSection>
</StructureSection>
== References ==
== References ==
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<ref>Aoki, M., Vinokur, J., Motoyama, K., Ishikawa, R., Collazo, M., Cascio, D., Sawaya, M. R., Ito, T., Bowie, J. U., & Hemmi, H. (2022). Crystal structure of mevalonate 3,5-bisphosphate decarboxylase reveals insight into the evolution of decarboxylases in the mevalonate metabolic pathways. The Journal of Biological Chemistry, 298(7), 102111–102111. https://doi.org/10.1016/j.jbc.2022.102111</ref>
<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-bisphosphate decarboxylase

Caption for this structure

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References 

 [1]
  1. ↑ Aoki, M., Vinokur, J., Motoyama, K., Ishikawa, R., Collazo, M., Cascio, D., Sawaya, M. R., Ito, T., Bowie, J. U., & Hemmi, H. (2022). Crystal structure of mevalonate 3,5-bisphosphate decarboxylase reveals insight into the evolution of decarboxylases in the mevalonate metabolic pathways. The Journal of Biological Chemistry, 298(7), 102111–102111. https://doi.org/10.1016/j.jbc.2022.102111
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