Sandbox Reserved 315: Difference between revisions
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=Introduction= | =Introduction= | ||
'''Orotidine monophosphate decarboxylase''' (ODCase), also known as '''orotidine 5’-monophosphate decarboxylase''' (OMP decarboxylase) or '''orotidine 5’-phosphate decarboxylase''' is an enzyme involved in | '''Orotidine monophosphate decarboxylase''' (ODCase), also known as '''orotidine 5’-monophosphate decarboxylase''' (OMP decarboxylase) or '''orotidine 5’-phosphate decarboxylase''', is an enzyme involved in nucleic acid biosynthesis. It catalyzes the conversion of orotidine 5’-monophosphate (OMP) to uridine 5’-monophosphate (UMP). This reaction is the final step in de novo pyrimidine nucleotide synthesis and is an essential precursor for both DNA and RNA. The main structure of orotidine monophosphate decarboxylase is a TIM barrel, with one side acting as the binding site, while the other side is closed-off. ODCase is often bound to other proteins in biological conditions. In single-cellular organisms, it can form a dimeric enzyme by binding to another ODCase<ref name = "Wu"/>. In multi-cellular organisms it can bind to orotate phosphoribosyltransferase to form a bifunctional protein<ref name = "Yablonski"/>. Additionally this enzyme has been studied for it’s remarkable catalytic efficiency<Ref name = "Miller">PMID:10681417</ref>. | ||
__TOC__ | __TOC__ | ||
{{STRUCTURE_1dv7 | PDB=1dv7 | SCENE=Sandbox_Reserved_315/Practice_representation/ | =Structure= | ||
< | <Structure load=1dv7 size='200' frame='true' align='left' caption='ODCase dimer' scene='Sandbox_Reserved_315/Odcase_dimer/1'/> | ||
{{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"/>. | |||
==Active Site== | ==Active Site== | ||
The <scene name='Sandbox_Reserved_315/Active_site/1'>active site</scene> is located in the opening of the TIM barrel. The ligand binds through extensive electrostatic interactions and hydrogen bonding with the ribose ring and phosphate group of OMP<ref name = "Wu"/>. Additionally, the active site forms a hydrophobic region around the pyrimidine ring of OMP <ref name = "Wu"/>. A unique feature of the active site is the series of alternating lysine and asparatate groups<ref name = "Wu"/>. This combination of basic and acidic groups contributes to binding, catalysis, and product release<ref name = "Wu"/>. The active site has both a hydrophobic pocket, which surrounds the pyrimidine base, and a hydration shell, which interacts with the phosphate group<ref name = "Wu"/>. This hydration shell involves several water molecules acting as bridges between the substrate and active site. | |||
=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 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>. | |||
[[Image:800px-OMPDC Reaction.png|center|frame|Decarboxylation of OMP to UMP]] | |||
==Biological Significance== | |||
All organisms carry out pyrimidine biosynthesis and therefore require orotidine monophosphate decarboxylase. ODCase activity is competitively inhibited by UMP and so partly regulates pyrimidine synthesis. Mutations in ODCase are genetically inherited and can cause [http://en.wikipedia.org/wiki/Orotic_aciduria orotic aciduria]<ref name = "Lee"/><ref name = "Brosnan"/>. This disorder is identified by orotic acid accumulation in the urine and can cause physical retardation and anemia<ref name = "Brosnan"/>. | |||
==UMP Synthase== | |||
In multicellular eukaryotes, orotidine monophosphate decarboxylase associates with orotate phosphoribosyltransferase to form a bifunctional protein, uridine monophosphate synthase [http://en.wikipedia.org/wiki/Uridine_monophosphate_synthetase uridine monophosphate synthase] (UMP synthase)<Ref name = "Lee"/><Ref name = "Yablonski"/>. UMP synthase carries out the last two steps in pyrimidine biosynthesis, converting orotate to uridine 5'-monophosphate<Ref name = "Yablonski">PMID:8631878</ref>. This reaction involves first adding ribose-P to orotate to form orotidine 5'-monophosphate, followed by a decarboxylation reaction to form uridine 5'-monophosphate<Ref name = "Yablonski"/>. In microorganisms these two enzymes are separate and coded by distinct genes. However research has shown that all known multicellular eukaryotes code the genes for these two enzymes together and as a result they are covalently bonded as a bifunctional protein with two distinct catalytic domains<Ref name = "Yablonski"/>. | |||
UMP synthase likely evolved in multicellular organisms for several reasons. It may increase efficiency of nucleotide synthesis by channeling the OMP intermediate from the first enzyme directly to the next<Ref name = "Yablonski"/>. Similarly, it improves allosteric control between the two domains<Ref name = "Yablonski"/>. It has also been shown that having a dimeric enzyme improves stability of both domains in UMP synthase compared to separate enzymes<Ref name = "Yablonski"/>. | |||
=Rate of Catalysis= | =Rate of Catalysis= | ||
ODCase is a strong catalyst for OMP decarboxylation. The decarboxylation of OMP to UMP has a halftime of 18 milliseconds when catalyzed by ODCase<Ref name = "Miller"/>. For this reaction to occur spontaneously it would take an astounding halftime of 78 million years<Ref name = "Miller"/>. This equates to a catalytic proficiency of 2.0 x 1023 M-1, making ODCase one of the most proficient catalytic enzymes known<Ref name = "Lee"/>. Additionally, ODCase achieves this catalytic power without the use of metals or other cofactors<Ref name = "Wu"/><Ref name = "Miller"/>. Instead, the catalytic efficiency is mainly achieved through destabilizing the reactive group on the substrate<Ref name = "Wu"/>. | |||
==Substrate Destabilization== | ==Substrate Destabilization== | ||
<Ref name = " | OMP is strongly attracted to the active site and further stabilized by phosphate and ribose interactions with ODCase<Ref name = "Wu"/>. However, the C¬¬6 carboxylate anion is strongly destabilized through repulsion by Asp70 and it is this destabilization that favors the decarboxylation reaction<Ref name = "Wu"/>. The simultaneous attraction and repulsion between the enzyme and substrate is known as the “Circe effect”, as described by William Jencks<Ref name = "Wu"/>. | ||
=References= | =References= | ||
<references/> | <references/> | ||