Sandbox Reserved 315: Difference between revisions
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{{STRUCTURE_1dv7 | PDB=1dv7 | SCENE=Sandbox_Reserved_315/Practice_representation/3 }} | {{STRUCTURE_1dv7 | PDB=1dv7 | SCENE=Sandbox_Reserved_315/Practice_representation/3 }} | ||
Orotidine monophosphate decarboxylase has a TIM barrel structure<Ref name = "Wu">PMID:10681441</ref><ref name = "Miller"/>. Like a typical TIM barrel, it is cylindrically-shaped as a result of parallel α helices and β sheets arranged in a circular manner. In biological conditions, ODCase is found in dimeric form, covalently bonded to a second ODCase<ref name = "Miller"/>. Each ODCase has 9 α helices that encompass 8 internal β sheets<ref name = "Wu"/><ref name = "Miller"/>. Both the C and N terminus are oriented on the same side of the monomer and directed away from the interface between the two monomers; this could explain how the enzymes can still maintain functionality when bound to another protein<ref name = "Miller"/>. The loops connecting these α helices and β sheets are where the active sites are found<ref name = "Miller"/>. The active site is only found on one side of the barrel, the “open” side, while the other side is closed off<ref name = "Miller"/>. | Orotidine monophosphate decarboxylase has a TIM barrel structure<Ref name = "Wu">PMID:10681441</ref><ref name = "Miller"/>. Like a typical TIM barrel, it is cylindrically-shaped as a result of parallel α helices and β sheets arranged in a circular manner. In biological conditions, ODCase is found in dimeric form, covalently bonded to a second ODCase<ref name = "Miller"/>. Each ODCase has 9 α helices that encompass 8 internal β sheets<ref name = "Wu"/><ref name = "Miller"/>. Both the C and N terminus are oriented on the same side of the monomer and directed away from the interface between the two monomers; this could explain how the enzymes can still maintain functionality when bound to another protein<ref name = "Miller"/>. The loops connecting these α helices and β sheets are where the active sites are found<ref name = "Miller"/>. The active site is only found on one side of the barrel, the “open” side, while the other side is closed off<ref name = "Miller"/>. | ||
==Active Site== | ==Active Site== | ||
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=Function= | =Function= | ||
Orotidine monophosphate decarboxylase is one of several proteins in de novo pyrimidine biosynthesis. Orotidine monophosphate (OMP) is formed when orotate reacts with 5-phosphoribosyl | Orotidine monophosphate decarboxylase is one of several proteins in de novo pyrimidine biosynthesis. Orotidine monophosphate (OMP) is formed when orotate reacts with 5-phosphoribosyl α-diphosphate (PRPP)<Ref name = "Brosnan">PMID:17513443</ref>. ODCase then decarboxylated OMP to form uridine monophosphate (UMP), which then goes on to be phosphorylated and converted into cytosine, uracil, and thymine<ref name = "Wu"/><ref name = "Brosnan"/>. | ||
The mechanism for decarboxylation of OMP is still unclear. Unlike other biochemical decarboxylation reactions that stabilize the reaction intermediate through delocalizing the electron pair, OCDase shows no such stabilization<ref name = "Lee"/>. One possible mechanism is the formation of a stabilized carbene intermediate resulting from protonization at the 4-C position of OMP<Ref name = "Lee">PMID:9139656</ref>. | The mechanism for decarboxylation of OMP is still unclear. Unlike other biochemical decarboxylation reactions that stabilize the reaction intermediate through delocalizing the electron pair, OCDase shows no such stabilization<ref name = "Lee"/>. One possible mechanism is the formation of a stabilized carbene intermediate resulting from protonization at the 4-C position of OMP<Ref name = "Lee">PMID:9139656</ref>. | ||
[[Image:800px-OMPDC Reaction.png|left|frame|Decarboxylation of OMP to UMP]] | |||
==Biological Significance== | ==Biological Significance== | ||