Sandbox Reserved 329: Difference between revisions
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== '''Uridylyl transferases''' == | == '''Uridylyl transferases''' == | ||
[[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.]] | [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|Figure 1. Secondary structure succession of TUT4 with bound ATP. Secondary structure residues are ordered from blue to red.]] | ||
== INTRODUCTION == | == INTRODUCTION == | ||
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== STRUCTURE == | == STRUCTURE == | ||
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> The signature active site motif for the polymerase β nucleotidyltransferase superfamily, including TUT4 is hG[G/S]X(9-13)Dh[D/E]h (where X is any amino acid, and h is hydrophobic amino acids).<ref name="second reference">PMID:11893335</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> The signature active site motif for the polymerase β nucleotidyltransferase superfamily, including TUT4 is hG [G/S]X(9-13)Dh[D/E]h (where X is any amino acid, and h is hydrophobic amino acids).<ref name="second reference">PMID:11893335</ref> | ||
[[Image:Signature_Motif.jpg|thumb|left|upright=2.0|Signature motif of the polymerase β | [[Image:Signature_Motif.jpg|thumb|left|upright=2.0|Figure 2. Signature motif of the polymerase β | ||
nucleotidyltransferase superfamily, as shown (green) in TUT4 with bound ATP.]] | nucleotidyltransferase superfamily, as shown (green) in TUT4 with bound ATP.]] | ||
== TRANSFERASE REACTION == | == TRANSFERASE REACTION == | ||
In the most general sense, the transferase reaction consists of the RNA substrate nucleophile (with some nucleotide selectivity) attacking the α-phosphorus atom of the nucleotide triphosphate [[ligand]].<ref name="primary citation">PMID:17785418</ref> The Mg<sup>2+</sup> ions are an important component of this reaction as one is thought to aid nucleophile deprotonation with the catalytic base (expected to be D136) and the other is thought to stabilize the leaving group (pyrophosphate).<ref name="primary citation">PMID:17785418</ref> However, due to steric constraints between the ATP [[ligand]] and the active site and RNA substrate, RNA binding is destabilized, thus slowing catalysis and the transfer of adenosine nucleotides.<ref name="primary citation">PMID:17785418</ref> | In the most general sense, the transferase reaction consists of the RNA substrate nucleophile (with some nucleotide selectivity) attacking the α-phosphorus atom of the nucleotide triphosphate [[ligand]].<ref name="primary citation">PMID:17785418</ref> The Mg<sup>2+</sup> ions are an important component of this reaction as one is thought to aid nucleophile deprotonation with the catalytic base (expected to be D136) and the other is thought to stabilize the leaving group (pyrophosphate).<ref name="primary citation">PMID:17785418</ref> However, due to steric constraints between the ATP [[ligand]] and the active site and RNA substrate, RNA binding is destabilized, thus slowing catalysis and the transfer of adenosine nucleotides.<ref name="primary citation">PMID:17785418</ref> | ||
== REFERENCES == | == REFERENCES == | ||
<references/> | <references/> | ||
== See Also == | |||
[[2q0d]] is TUT4 with bound ATP | |||
== External Links == | == External Links == | ||
[http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank] | [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank: TUT4 with bound ATP] | ||
[http://www.rcsb.org/pdb/explore.do?structureId=2Q0C RCSB Protein Data Bank: TUT4 with bound CTP] | |||
[http://www.rcsb.org/pdb/explore.do?structureId=2Q0F RCSB Protein Data Bank: TUT4 with bound UTP and UMP] | |||
[http://www.rcsb.org/pdb/explore.do?structureId=2Q0E RCSB Protein Data Bank: TUT4 with bound GTP] | |||
[http://www.rcsb.org/pdb/explore.do?structureId=2Q0G RCSB Protein Data Bank: TUT4 with bound UpU] | |||
