User:Adam Mirando/Sandbox 1: Difference between revisions

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[[Image:Xanthine Mechanism.png|thumb|center|1000px|'''Xanthine oxidation mechanism.''' Adapted from Nishino ''et al.'' ''FEBS Journal.'' (2008) 275, 3278-3289]]

Several mechanisms have been suggested for the oxidation of xanthine to urate by xanthine oxidoreductase. However, a substantial amount of data appears to favor a mechanism in which a deprotonated molybdenum hydroxyl attacks the C8 atom of xanthine. This mechanism begins with the extraction of a proton from the hydroxyl of the molybdenum center by Glu1261 <ref>PMID:15265866</ref>, an event computed to occur readily in the presence of the substrate <ref name="theoretical">PMID:17564439</ref>. The electrons from the deprotonated oxygen are then free to attack the electrophilic C8 atom of the bound <scene name='User:Adam_Mirando/Sandbox_1/Xanthine_in_active_site/1'>xanthine</scene>. The formation of glutamic acid stabilizes this structure through hydrogen bond interactions with the N1 atom <ref>PMID:15148401</ref>. Crystalographic data has also suggested possible stabilizing interactions between Arg880 of the active site and enolate tautomerization at C6 <ref name="SubOri">PMID:19109252</ref>. Bond formation between the substrate and the molybdenum center orients a Mo = S moiety equatorially to the substrate, positioning it favorably for a concomitant hydride transfer from xanthine N7 <ref name="gluarg">PMID:18513323</ref>. Extraction of this hydride produces Mo-SH and reduces the Mo center from Mo VI to Mo IV. This intermediate breaks down through electron transfer from the molybdenum center through the iron-sulfur clusters, known as Fe-S I and Fe-S II to the bound FAD, forming FADH2. In this mechanism the Fe-S clusters function as electron sinks, maintaining an oxidized Mo-cofactor and a reduced FADH2. The Mo atom serves as a transducer between the two electrons passed from the substrate to the single electron of system of the Fe-S clusters. The transfer of electrons can be monitored through the formation of the paramagnetic transient Mo V <ref>PMID:15134930</ref>. Subsequent reduction of NAD+ to NADH in the case of xanthine dehydrogenases and O2 to H2O2 regenerates the oxidized FAD. Other mechanisms involving protonated molybdenum hydroxyls have been proposed with similar calculated activation energies (40 kcal/mol). However, the products in these cases have been computationally determined to be less stable that the reactant complex <ref name="theoretical" />.

Several mechanisms have been suggested for the oxidation of xanthine to urate by xanthine oxidoreductase. However, a substantial amount of data appears to favor a mechanism in which a deprotonated molybdenum hydroxyl attacks the C8 atom of xanthine. This mechanism begins with the extraction of a proton from the hydroxyl of the molybdenum center by Glu1261 <ref>PMID:15265866</ref>, an event computed to occur readily in the presence of the substrate <ref name="theoretical">PMID:17564439</ref>. The electrons from the deprotonated oxygen are then free to attack the electrophilic C8 atom of the bound <scene name='User:Adam_Mirando/Sandbox_1/Xanthine_in_active_site/1'>xanthine</scene>. The formation of glutamic acid stabilizes this structure through hydrogen bond interactions with the N1 atom <ref>PMID:15148401</ref>. Crystalographic data has also suggested possible stabilizing interactions between Arg880 of the active site and enolate tautomerization at C6 <ref name="SubOri">PMID:19109252</ref>. Bond formation between the substrate and the molybdenum center orients a Mo = S moiety equatorially to the substrate, positioning it favorably for a concomitant hydride transfer from xanthine N7 <ref name="gluarg">PMID:18513323</ref>. Extraction of this hydride produces Mo-SH and reduces the Mo center from Mo VI to Mo IV. This intermediate breaks down through electron transfer from the molybdenum center through the iron-sulfur clusters, known as Fe-S I and Fe-S II to the bound FAD, forming FADH2. In this mechanism the Fe-S clusters function as electron sinks, maintaining an oxidized Mo-cofactor and a reduced FADH2. The Mo atom serves as a transducer between the two electrons passed from the substrate to the single electron of system of the Fe-S clusters. The transfer of electrons can be monitored through the formation of the paramagnetic transient Mo V <ref>PMID:15134930</ref>. Subsequent reduction of NAD+ to NADH in the case of xanthine dehydrogenases and O2 to H2O2 and superoxide for the oxidase regenerates the oxidized FAD. Other mechanisms involving protonated molybdenum hydroxyls have been proposed with similar calculated activation energies (40 kcal/mol). However, the products in these cases have been computationally determined to be less stable that the reactant complex <ref name="theoretical" />.

===Hypoxanthine Oxidation Mechanism===

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 [[Image:Xanthine Mechanism.png|thumb|center|1000px|'''Xanthine oxidation mechanism.''' Adapted from Nishino ''et al.'' ''FEBS Journal.'' (2008) 275, 3278-3289]]
-Several mechanisms have been suggested for the oxidation of xanthine to urate by xanthine oxidoreductase. However, a substantial amount of data appears to favor a mechanism in which a deprotonated molybdenum hydroxyl attacks the C8 atom of xanthine. This mechanism begins with the extraction of a proton from the hydroxyl of the molybdenum center by Glu1261 <ref>PMID:15265866</ref>, an event computed to occur readily in the presence of the substrate <ref name="theoretical">PMID:17564439</ref>. The electrons from the deprotonated oxygen are then free to attack the electrophilic C8 atom of the bound <scene name='User:Adam_Mirando/Sandbox_1/Xanthine_in_active_site/1'>xanthine</scene>. The formation of glutamic acid stabilizes this structure through hydrogen bond interactions with the N1 atom <ref>PMID:15148401</ref>. Crystalographic data has also suggested possible stabilizing interactions between Arg880 of the active site and enolate tautomerization at C6 <ref name="SubOri">PMID:19109252</ref>. Bond formation between the substrate and the molybdenum center orients a Mo = S moiety equatorially to the substrate, positioning it favorably for a concomitant hydride transfer from xanthine N7 <ref name="gluarg">PMID:18513323</ref>. Extraction of this hydride produces Mo-SH and reduces the Mo center from Mo VI to Mo IV. This intermediate breaks down through electron transfer from the molybdenum center through the iron-sulfur clusters, known as Fe-S I and Fe-S II to the bound FAD, forming FADH<sub>2</sub>. In this mechanism the Fe-S clusters function as electron sinks, maintaining an oxidized Mo-cofactor and a reduced FADH<sub>2</sub>. The Mo atom serves as a transducer between the two electrons passed from the substrate to the single electron of system of the Fe-S clusters.  The transfer of electrons can be monitored through the formation of the paramagnetic transient Mo V <ref>PMID:15134930</ref>. Subsequent reduction of NAD<sup>+</sup> to NADH in the case of xanthine dehydrogenases and O<sub>2</sub> to H<sub>2</sub>O<sub>2</sub> regenerates the oxidized FAD. Other mechanisms involving protonated molybdenum hydroxyls have been proposed with similar calculated activation energies (40 kcal/mol). However, the products in these cases have been computationally determined to be less stable that the reactant complex <ref name="theoretical" />.
+Several mechanisms have been suggested for the oxidation of xanthine to urate by xanthine oxidoreductase. However, a substantial amount of data appears to favor a mechanism in which a deprotonated molybdenum hydroxyl attacks the C8 atom of xanthine. This mechanism begins with the extraction of a proton from the hydroxyl of the molybdenum center by Glu1261 <ref>PMID:15265866</ref>, an event computed to occur readily in the presence of the substrate <ref name="theoretical">PMID:17564439</ref>. The electrons from the deprotonated oxygen are then free to attack the electrophilic C8 atom of the bound <scene name='User:Adam_Mirando/Sandbox_1/Xanthine_in_active_site/1'>xanthine</scene>. The formation of glutamic acid stabilizes this structure through hydrogen bond interactions with the N1 atom <ref>PMID:15148401</ref>. Crystalographic data has also suggested possible stabilizing interactions between Arg880 of the active site and enolate tautomerization at C6 <ref name="SubOri">PMID:19109252</ref>. Bond formation between the substrate and the molybdenum center orients a Mo = S moiety equatorially to the substrate, positioning it favorably for a concomitant hydride transfer from xanthine N7 <ref name="gluarg">PMID:18513323</ref>. Extraction of this hydride produces Mo-SH and reduces the Mo center from Mo VI to Mo IV. This intermediate breaks down through electron transfer from the molybdenum center through the iron-sulfur clusters, known as Fe-S I and Fe-S II to the bound FAD, forming FADH<sub>2</sub>. In this mechanism the Fe-S clusters function as electron sinks, maintaining an oxidized Mo-cofactor and a reduced FADH<sub>2</sub>. The Mo atom serves as a transducer between the two electrons passed from the substrate to the single electron of system of the Fe-S clusters.  The transfer of electrons can be monitored through the formation of the paramagnetic transient Mo V <ref>PMID:15134930</ref>. Subsequent reduction of NAD<sup>+</sup> to NADH in the case of xanthine dehydrogenases and O<sub>2</sub> to H<sub>2</sub>O<sub>2</sub> and superoxide for the oxidase regenerates the oxidized FAD. Other mechanisms involving protonated molybdenum hydroxyls have been proposed with similar calculated activation energies (40 kcal/mol). However, the products in these cases have been computationally determined to be less stable that the reactant complex <ref name="theoretical" />.
 ===Hypoxanthine Oxidation Mechanism===