Sandbox Reserved 329: Difference between revisions
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== '''Uridylyl transferases''' == | == '''Uridylyl transferases''' == | ||
[[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0| | [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|Secondary structure succession of TUT4 with bound ATP. Secondary structure residues are ordered from blue to red.]] | ||
== INTRODUCTION == | == INTRODUCTION == | ||
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TUT4 with a bound <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> (consisting of an ATP molecule and two Mg<sup>2+</sup> ions) has little π-electron stacking with both the active site <scene name='Sandbox_Reserved_329/Tyr189/1'>tyrosine residue</scene> (Y189) and the RNA substrate, and so is destabilizing, however the phosphate groups of the ATP have been shown to superpose well with that of the other ligands.<ref name="primary citation">PMID:17785418</ref> The Mg<sup>2+</sup> ions are coordinated by three <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> (D66, D68, and D136) which are conserved among TUTases, and thus vital in the transferase reaction.<ref name="primary citation">PMID:17785418</ref> Hydrogen bonding and hydrophobic interactions are important in the binding of the RNA substrate to the enzyme as well as the binding of the ligand to the apo protein. Notably, hydrogen bonding interactions occur among <scene name='Sandbox_Reserved_329/Hydrophobic_hbond_interactions/1'>R121, D68, and D136</scene> of TUT4 with the RNA substrate, and among <scene name='Sandbox_Reserved_329/Interactions_atp/1'>S148, Y189, and N147</scene> of the apo protein with the ATP complex.<ref name="primary citation">PMID:17785418</ref> Hydrophobic interactions with the RNA substrate and <scene name='Sandbox_Reserved_329/Hydrophobic_hbond_interactions/1'>V122</scene> of TUT4 also contribute to the transferase reaction.<ref name="primary citation">PMID:17785418</ref> The lack of triple stacking as well as different hydrogen bonding interactions contribute to the preference of TUT4 for UTP instead of ATP, however it is thought that minimal mutations would be required for TUT4 to become ATP specific. <ref name="primary citation">PMID:17785418</ref> | TUT4 with a bound <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> (consisting of an ATP molecule and two Mg<sup>2+</sup> ions) has little π-electron stacking with both the active site <scene name='Sandbox_Reserved_329/Tyr189/1'>tyrosine residue</scene> (Y189) and the RNA substrate, and so is destabilizing, however the phosphate groups of the ATP have been shown to superpose well with that of the other ligands.<ref name="primary citation">PMID:17785418</ref> The Mg<sup>2+</sup> ions are coordinated by three <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> (D66, D68, and D136) which are conserved among TUTases, and thus vital in the transferase reaction.<ref name="primary citation">PMID:17785418</ref> Hydrogen bonding and hydrophobic interactions are important in the binding of the RNA substrate to the enzyme as well as the binding of the ligand to the apo protein. Notably, hydrogen bonding interactions occur among <scene name='Sandbox_Reserved_329/Hydrophobic_hbond_interactions/1'>R121, D68, and D136</scene> of TUT4 with the RNA substrate, and among <scene name='Sandbox_Reserved_329/Interactions_atp/1'>S148, Y189, and N147</scene> of the apo protein with the ATP complex.<ref name="primary citation">PMID:17785418</ref> Hydrophobic interactions with the RNA substrate and <scene name='Sandbox_Reserved_329/Hydrophobic_hbond_interactions/1'>V122</scene> of TUT4 also contribute to the transferase reaction.<ref name="primary citation">PMID:17785418</ref> The lack of triple stacking as well as different hydrogen bonding interactions contribute to the preference of TUT4 for UTP instead of ATP, however it is thought that minimal mutations would be required for TUT4 to become ATP specific. <ref name="primary citation">PMID:17785418</ref> | ||
[[Image:Signature_Motif.jpg|thumb|left|upright=2.0|Signature motif of the polymerase β � | |||
nucleotidyltransferase superfamily, as shown (in green) in TUT4 with bound ATP.]] | |||
== TRANSFERASE REACTION == | == TRANSFERASE REACTION == | ||
