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https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Jessica+Lowry Proteopedia - User contributions [en] 2026-09-16T00:48:10Z User contributions MediaWiki 1.43.8 https://proteopedia.org/index.php?title=Terminal_Uridylyl_Transferase&diff=2498348 Terminal Uridylyl Transferase 2015-11-21T19:54:58Z

<p>Jessica Lowry: </p> <hr /> <div><br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[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.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> '''Terminal uridylyl transferases''' (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites that cause diseases in humans such as African Sleeping Sickness. It has been suggested that the knowledge of TUTases may aid in the treatment of these diseases as TUTases function in RNA editing in these parasites, and thus can serve as enzymes to target.<ref name="second reference">PMID:11893335</ref> More specifically TUT4 catalyzes a reaction that adds a nucleotide, from a nucleotide triphosphate, to uridine monophosphate (UMP), the minimally required terminal RNA substrate.<ref name="primary citation">PMID:17785418</ref> TUTase4 is able to bind to the nucleotide triphosphates ATP, CTP, GTP or UTP, however, UTP and CTP are preferred, whereas ATP and GTP [[ligand]]s have been shown to cause a significant decrease in enzymatic activity.<ref name="primary citation">PMID:17785418</ref> The preference for UTP causes TUTase4 to typically add a uracil nucleotide to the RNA substrate. This selectivity has a variety of mechanisms, including a loss of coplanarity (π-electron stacking) between the ATP and a tyrosine of the active site (Y189) required for catalysis, and reduced stacking between the UMP and ATP rings.<ref name="primary citation">PMID:17785418</ref> The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg<sup>2+</sup> ions required by the ligand.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> 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&nbsp;[G/S]X(9-13)Dh[D/E]h (where X designates any amino acid, and h designates hydrophobic amino acids).<ref name="second reference">PMID:11893335</ref><br /> <br /> [[Image:Signature_Motif.jpg|thumb|left|upright=2.0|Figure 2. Signature motif of the polymerase β<br /> nucleotidyltransferase superfamily, as shown (green) in TUT4 with bound ATP.]]<br /> <br /> <br /> <br /> == TRANSFERASE REACTION ==<br /> <br /> 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><br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == See Also ==<br /> <br /> [[2q0d]] is TUT4 with bound ATP<br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank: TUT4 with bound ATP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0C RCSB Protein Data Bank: TUT4 with bound CTP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0F RCSB Protein Data Bank: TUT4 with bound UTP and UMP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0E RCSB Protein Data Bank: TUT4 with bound GTP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0G RCSB Protein Data Bank: TUT4 with bound UpU]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Terminal_Uridylyl_Transferase&diff=1393637 Terminal Uridylyl Transferase 2012-05-17T19:15:35Z

<p>Jessica Lowry: </p> <hr /> <div><br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[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.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites that cause diseases in humans such as African Sleeping Sickness. It has been suggested that the knowledge of TUTases may aid in the treatment of these diseases as TUTases function in RNA editing in these parasites, and thus can serve as enzymes to target.<ref name="second reference">PMID:11893335</ref> More specifically TUT4 catalyzes a reaction that adds a nucleotide, from a nucleotide triphosphate, to uridine monophosphate (UMP), the minimally required terminal RNA substrate.<ref name="primary citation">PMID:17785418</ref> TUTase4 is able to bind to the nucleotide triphosphates ATP, CTP, GTP or UTP, however, UTP and CTP are preferred, whereas ATP and GTP [[ligand]]s have been shown to cause a significant decrease in enzymatic activity.<ref name="primary citation">PMID:17785418</ref> The preference for UTP causes TUTase4 to typically add a uracil nucleotide to the RNA substrate. This selectivity has a variety of mechanisms, including a loss of coplanarity (π-electron stacking) between the ATP and a tyrosine of the active site (Y189) required for catalysis, and reduced stacking between the UMP and ATP rings.<ref name="primary citation">PMID:17785418</ref> The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg<sup>2+</sup> ions required by the ligand.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> 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&nbsp;[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><br /> <br /> [[Image:Signature_Motif.jpg|thumb|left|upright=2.0|Figure 2. Signature motif of the polymerase β<br /> nucleotidyltransferase superfamily, as shown (green) in TUT4 with bound ATP.]]<br /> <br /> <br /> <br /> == TRANSFERASE REACTION ==<br /> <br /> 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><br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == See Also ==<br /> <br /> [[2q0d]] is TUT4 with bound ATP<br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank: TUT4 with bound ATP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0C RCSB Protein Data Bank: TUT4 with bound CTP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0F RCSB Protein Data Bank: TUT4 with bound UTP and UMP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0E RCSB Protein Data Bank: TUT4 with bound GTP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0G RCSB Protein Data Bank: TUT4 with bound UpU]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Terminal_Uridylyl_Transferase&diff=1393636 Terminal Uridylyl Transferase 2012-05-17T19:15:15Z

<p>Jessica Lowry: </p> <hr /> <div><br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[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.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites that cause diseases in humans such as African Sleeping Sickness. It has been suggested that the knowledge of TUTases may aid in the treatment of these diseases as TUTases function in RNA editing in these parasites, and thus can serve as enzymes to target.<ref name="second reference">PMID:11893335</ref> More specifically TUT4 catalyzes a reaction that adds a nucleotide, from a nucleotide triphosphate, to uridine monophosphate (UMP), the minimally required terminal RNA substrate.<ref name="primary citation">PMID:17785418</ref> TUTase4 is able to bind to the nucleotide triphosphates ATP, CTP, GTP or UTP, however, UTP and CTP are preferred, whereas ATP and GTP [[ligand]]s have been shown to cause a significant decrease in enzymatic activity.<ref name="primary citation">PMID:17785418</ref> The preference for UTP causes TUTase4 to typically add a uracil nucleotide to the RNA substrate. This selectivity has a variety of mechanisms, including a loss of coplanarity (π-electron stacking) between the ATP and a tyrosine of the active site (Y189) required for catalysis, and reduced stacking between the UMP and ATP rings.<ref name="primary citation">PMID:17785418</ref> The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg<sup>2+</sup> ions required by the ligand.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> 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&nbsp;[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><br /> <br /> [[Image:Signature_Motif.jpg|thumb|left|upright=2.0|Figure 2. Signature motif of the polymerase β<br /> nucleotidyltransferase superfamily, as shown (green) in TUT4 with bound ATP.]]<br /> <br /> <br /> <br /> == TRANSFERASE REACTION ==<br /> <br /> 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><br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == See Also ==<br /> <br /> [[2q0d]] is TUT4 with bound ATP<br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank: TUT4 with bound ATP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0C RCSB Protein Data Bank: TUT4 with bound CTP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0F RCSB Protein Data Bank: TUT4 with bound UTP and UMP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0E RCSB Protein Data Bank: TUT4 with bound GTP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0G RCSB Protein Data Bank: TUT4 with bound UpU]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Terminal_Uridylyl_Transferase&diff=1393635 Terminal Uridylyl Transferase 2012-05-17T19:14:51Z

<p>Jessica Lowry: </p> <hr /> <div><br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[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.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites that cause diseases in humans such as African Sleeping Sickness. It has been suggested that the knowledge of TUTases may aid in the treatment of these diseases as TUTases function in RNA editing in these parasites, and thus can serve as enzymes to target.<ref name="second reference">PMID:11893335</ref> More specifically TUT4 catalyzes a reaction that adds a nucleotide, from a nucleotide triphosphate, to uridine monophosphate (UMP), the minimally required terminal RNA substrate.<ref name="primary citation">PMID:17785418</ref> TUTase4 is able to bind to the nucleotide triphosphates ATP, CTP, GTP or UTP, however, UTP and CTP are preferred, whereas ATP and GTP [[ligand]]s have been shown to cause a significant decrease in enzymatic activity.<ref name="primary citation">PMID:17785418</ref> The preference for UTP causes TUTase4 to typically add a uracil nucleotide to the RNA substrate. This selectivity has a variety of mechanisms, including a loss of coplanarity (π-electron stacking) between the ATP and a tyrosine of the active site (Y189) required for catalysis, and reduced stacking between the UMP and ATP rings.<ref name="primary citation">PMID:17785418</ref> The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg<sup>2+</sup> ions required by the ligand.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> 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&nbsp;[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><br /> <br /> [[Image:Signature_Motif.jpg|thumb|left|upright=2.0|Figure 2. Signature motif of the polymerase β<br /> nucleotidyltransferase superfamily, as shown (green) in TUT4 with bound ATP.]]<br /> <br /> <br /> <br /> == TRANSFERASE REACTION ==<br /> <br /> 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><br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == See Also ==<br /> <br /> [[2q0d]] is TUT4 with bound ATP<br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank: TUT4 with bound ATP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0C RCSB Protein Data Bank: TUT4 with bound CTP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0F RCSB Protein Data Bank: TUT4 with bound UTP and UMP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0E RCSB Protein Data Bank: TUT4 with bound GTP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0G RCSB Protein Data Bank: TUT4 with bound UpU]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Terminal_Uridylyl_Transferase&diff=1393634 Terminal Uridylyl Transferase 2012-05-17T18:58:39Z

<p>Jessica Lowry: New page: <br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[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.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites that cause diseases in humans such as African Sleeping Sickness. It has been suggested that the knowledge of TUTases may aid in the treatment of these diseases as TUTases function in RNA editing in these parasites, and thus can serve as enzymes to target.<ref name="second reference">PMID:11893335</ref> More specifically TUT4 catalyzes a reaction that adds a nucleotide, from a nucleotide triphosphate, to uridine monophosphate (UMP), the minimally required terminal RNA substrate.<ref name="primary citation">PMID:17785418</ref> TUTase4 is able to bind to the nucleotide triphosphates ATP, CTP, GTP or UTP, however, UTP and CTP are preferred, whereas ATP and GTP [[ligand]]s have been shown to cause a significant decrease in enzymatic activity.<ref name="primary citation">PMID:17785418</ref> The preference for UTP causes TUTase4 to typically add a uracil nucleotide to the RNA substrate. This selectivity has a variety of mechanisms, including a loss of coplanarity (π-electron stacking) between the ATP and a tyrosine of the active site (Y189) required for catalysis, and reduced stacking between the UMP and ATP rings.<ref name="primary citation">PMID:17785418</ref> The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg<sup>2+</sup> ions required by the ligand.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> 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&nbsp;[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><br /> <br /> [[Image:Signature_Motif.jpg|thumb|left|upright=2.0|Figure 2. Signature motif of the polymerase β<br /> nucleotidyltransferase superfamily, as shown (green) in TUT4 with bound ATP.]]<br /> <br /> <br /> <br /> == TRANSFERASE REACTION ==<br /> <br /> 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><br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == See Also ==<br /> <br /> [[2q0d]] is TUT4 with bound ATP<br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank: TUT4 with bound ATP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0C RCSB Protein Data Bank: TUT4 with bound CTP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0F RCSB Protein Data Bank: TUT4 with bound UTP and UMP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0E RCSB Protein Data Bank: TUT4 with bound GTP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0G RCSB Protein Data Bank: TUT4 with bound UpU]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Terminal_Uridylyl_Transferase_4&diff=1393633 Terminal Uridylyl Transferase 4 2012-05-17T18:56:11Z

<p>Jessica Lowry: Terminal Uridylyl Transferase 4 moved to Sandbox Reserved 329 over redirect</p> <hr /> <div>#REDIRECT [[Sandbox Reserved 329]]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Sandbox_Reserved_329&diff=1393632 Sandbox Reserved 329 2012-05-17T18:56:11Z

<p>Jessica Lowry: Terminal Uridylyl Transferase 4 moved to Sandbox Reserved 329 over redirect</p> <hr /> <div><br /> {{Template:Sandbox_Reserved_BCMB307}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[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.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites that cause diseases in humans such as African Sleeping Sickness. It has been suggested that the knowledge of TUTases may aid in the treatment of these diseases as TUTases function in RNA editing in these parasites, and thus can serve as enzymes to target.<ref name="second reference">PMID:11893335</ref> More specifically TUT4 catalyzes a reaction that adds a nucleotide, from a nucleotide triphosphate, to uridine monophosphate (UMP), the minimally required terminal RNA substrate.<ref name="primary citation">PMID:17785418</ref> TUTase4 is able to bind to the nucleotide triphosphates ATP, CTP, GTP or UTP, however, UTP and CTP are preferred, whereas ATP and GTP [[ligand]]s have been shown to cause a significant decrease in enzymatic activity.<ref name="primary citation">PMID:17785418</ref> The preference for UTP causes TUTase4 to typically add a uracil nucleotide to the RNA substrate. This selectivity has a variety of mechanisms, including a loss of coplanarity (π-electron stacking) between the ATP and a tyrosine of the active site (Y189) required for catalysis, and reduced stacking between the UMP and ATP rings.<ref name="primary citation">PMID:17785418</ref> The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg<sup>2+</sup> ions required by the ligand.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> 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&nbsp;[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><br /> <br /> [[Image:Signature_Motif.jpg|thumb|left|upright=2.0|Figure 2. Signature motif of the polymerase β<br /> nucleotidyltransferase superfamily, as shown (green) in TUT4 with bound ATP.]]<br /> <br /> <br /> <br /> == TRANSFERASE REACTION ==<br /> <br /> 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><br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == See Also ==<br /> <br /> [[2q0d]] is TUT4 with bound ATP<br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank: TUT4 with bound ATP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0C RCSB Protein Data Bank: TUT4 with bound CTP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0F RCSB Protein Data Bank: TUT4 with bound UTP and UMP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0E RCSB Protein Data Bank: TUT4 with bound GTP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0G RCSB Protein Data Bank: TUT4 with bound UpU]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Sandbox_Reserved_329&diff=1393630 Sandbox Reserved 329 2012-05-17T18:49:17Z

<p>Jessica Lowry: Sandbox Reserved 329 moved to Terminal Uridylyl Transferase 4: Moving from a reserved sandbox, due to page being completed.</p> <hr /> <div><br /> {{Template:Sandbox_Reserved_BCMB307}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[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.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites that cause diseases in humans such as African Sleeping Sickness. It has been suggested that the knowledge of TUTases may aid in the treatment of these diseases as TUTases function in RNA editing in these parasites, and thus can serve as enzymes to target.<ref name="second reference">PMID:11893335</ref> More specifically TUT4 catalyzes a reaction that adds a nucleotide, from a nucleotide triphosphate, to uridine monophosphate (UMP), the minimally required terminal RNA substrate.<ref name="primary citation">PMID:17785418</ref> TUTase4 is able to bind to the nucleotide triphosphates ATP, CTP, GTP or UTP, however, UTP and CTP are preferred, whereas ATP and GTP [[ligand]]s have been shown to cause a significant decrease in enzymatic activity.<ref name="primary citation">PMID:17785418</ref> The preference for UTP causes TUTase4 to typically add a uracil nucleotide to the RNA substrate. This selectivity has a variety of mechanisms, including a loss of coplanarity (π-electron stacking) between the ATP and a tyrosine of the active site (Y189) required for catalysis, and reduced stacking between the UMP and ATP rings.<ref name="primary citation">PMID:17785418</ref> The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg<sup>2+</sup> ions required by the ligand.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> 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&nbsp;[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><br /> <br /> [[Image:Signature_Motif.jpg|thumb|left|upright=2.0|Figure 2. Signature motif of the polymerase β<br /> nucleotidyltransferase superfamily, as shown (green) in TUT4 with bound ATP.]]<br /> <br /> <br /> <br /> == TRANSFERASE REACTION ==<br /> <br /> 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><br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == See Also ==<br /> <br /> [[2q0d]] is TUT4 with bound ATP<br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank: TUT4 with bound ATP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0C RCSB Protein Data Bank: TUT4 with bound CTP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0F RCSB Protein Data Bank: TUT4 with bound UTP and UMP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0E RCSB Protein Data Bank: TUT4 with bound GTP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0G RCSB Protein Data Bank: TUT4 with bound UpU]</div>

Jessica Lowry https://proteopedia.org/index.php?title=User:Jessica_Lowry&diff=1297222 User:Jessica Lowry 2011-09-20T04:19:19Z

<p>Jessica Lowry: </p> <hr /> <div>4th year Undergraduate student, majoring in Biochemistry and Molecular Biology.</div>

Jessica Lowry https://proteopedia.org/index.php?title=Sandbox_Reserved_329&diff=1224662 Sandbox Reserved 329 2011-04-04T01:40:38Z

<p>Jessica Lowry: </p> <hr /> <div><br /> {{Template:Sandbox_Reserved_BCMB307}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[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.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites that cause diseases in humans such as African Sleeping Sickness. It has been suggested that the knowledge of TUTases may aid in the treatment of these diseases as TUTases function in RNA editing in these parasites, and thus can serve as enzymes to target.<ref name="second reference">PMID:11893335</ref> More specifically TUT4 catalyzes a reaction that adds a nucleotide, from a nucleotide triphosphate, to uridine monophosphate (UMP), the minimally required terminal RNA substrate.<ref name="primary citation">PMID:17785418</ref> TUTase4 is able to bind to the nucleotide triphosphates ATP, CTP, GTP or UTP, however, UTP and CTP are preferred, whereas ATP and GTP [[ligand]]s have been shown to cause a significant decrease in enzymatic activity.<ref name="primary citation">PMID:17785418</ref> The preference for UTP causes TUTase4 to typically add a uracil nucleotide to the RNA substrate. This selectivity has a variety of mechanisms, including a loss of coplanarity (π-electron stacking) between the ATP and a tyrosine of the active site (Y189) required for catalysis, and reduced stacking between the UMP and ATP rings.<ref name="primary citation">PMID:17785418</ref> The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg<sup>2+</sup> ions required by the ligand.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> 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&nbsp;[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><br /> <br /> [[Image:Signature_Motif.jpg|thumb|left|upright=2.0|Figure 2. Signature motif of the polymerase β<br /> nucleotidyltransferase superfamily, as shown (green) in TUT4 with bound ATP.]]<br /> <br /> <br /> <br /> == TRANSFERASE REACTION ==<br /> <br /> 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><br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == See Also ==<br /> <br /> [[2q0d]] is TUT4 with bound ATP<br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank: TUT4 with bound ATP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0C RCSB Protein Data Bank: TUT4 with bound CTP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0F RCSB Protein Data Bank: TUT4 with bound UTP and UMP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0E RCSB Protein Data Bank: TUT4 with bound GTP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0G RCSB Protein Data Bank: TUT4 with bound UpU]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Sandbox_Reserved_329&diff=1224643 Sandbox Reserved 329 2011-04-04T01:33:20Z

<p>Jessica Lowry: </p> <hr /> <div><br /> {{Template:Sandbox_Reserved_BCMB307}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[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.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites that cause diseases in humans such as African Sleeping Sickness. It has been suggested that the knowledge of TUTases may aid in the treatment of these diseases as TUTases function in RNA editing in these parasites, and thus can serve as enzymes to target.<ref name="second reference">PMID:11893335</ref> More specifically TUT4 catalyzes a reaction that adds a nucleotide, from a nucleotide triphosphate, to uridine monophosphate (UMP), the minimally required terminal RNA substrate.<ref name="primary citation">PMID:17785418</ref> TUTase4 is able to bind to the nucleotide triphosphates ATP, CTP, GTP or UTP, however, UTP and CTP are preferred, whereas ATP and GTP [[ligand]]s have been shown to cause a significant decrease in enzymatic activity.<ref name="primary citation">PMID:17785418</ref> The preference for UTP causes TUTase4 to typically add a uracil nucleotide to the RNA substrate. This selectivity has a variety of mechanisms, including a loss of coplanarity (π-electron stacking) between the ATP and a tyrosine of the active site (Y189) required for catalysis, and reduced stacking between the UMP and ATP rings.<ref name="primary citation">PMID:17785418</ref> The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg<sup>2+</sup> ions required by the ligand.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> 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&nbsp;[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><br /> <br /> [[Image:Signature_Motif.jpg|thumb|left|upright=2.0|Signature motif of the polymerase β<br /> nucleotidyltransferase superfamily, as shown (green) in TUT4 with bound ATP.]]<br /> <br /> == TRANSFERASE REACTION ==<br /> <br /> 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><br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == See Also ==<br /> <br /> [[2q0d]] is TUT4 with bound ATP<br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank: TUT4 with bound ATP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0C RCSB Protein Data Bank: TUT4 with bound CTP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0F RCSB Protein Data Bank: TUT4 with bound UTP and UMP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0E RCSB Protein Data Bank: TUT4 with bound GTP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0G RCSB Protein Data Bank: TUT4 with bound UpU]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Sandbox_Reserved_329&diff=1224631 Sandbox Reserved 329 2011-04-04T01:25:31Z

<p>Jessica Lowry: </p> <hr /> <div><br /> {{Template:Sandbox_Reserved_BCMB307}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[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.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites that cause diseases in humans such as African Sleeping Sickness. It has been suggested that the knowledge of TUTases may aid in the treatment of these diseases as TUTases function in RNA editing in these parasites, and thus can serve as enzymes to target.<ref name="second reference">PMID:11893335</ref> More specifically TUT4 catalyzes a reaction that adds a nucleotide, from a nucleotide triphosphate, to uridine monophosphate (UMP), the minimally required terminal RNA substrate.<ref name="primary citation">PMID:17785418</ref> TUTase4 is able to bind to the nucleotide triphosphates ATP, CTP, GTP or UTP, however, UTP and CTP are preferred, whereas ATP and GTP [[ligand]]s have been shown to cause a significant decrease in enzymatic activity.<ref name="primary citation">PMID:17785418</ref> The preference for UTP causes TUTase4 to typically add a uracil nucleotide to the RNA substrate. This selectivity has a variety of mechanisms, including a loss of coplanarity (π-electron stacking) between the ATP and a tyrosine of the active site (Y189) required for catalysis, and reduced stacking between the UMP and ATP rings.<ref name="primary citation">PMID:17785418</ref> The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg<sup>2+</sup> ions required by the ligand.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> 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&nbsp;[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><br /> <br /> [[Image:Signature_Motif.jpg|thumb|left|upright=2.0|Signature motif of the polymerase β<br /> nucleotidyltransferase superfamily, as shown (green) in TUT4 with bound ATP.]]<br /> <br /> == TRANSFERASE REACTION ==<br /> <br /> 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><br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank: TUT4 with bound ATP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0C RCSB Protein Data Bank: TUT4 with bound CTP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0F RCSB Protein Data Bank: TUT4 with bound UTP and UMP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0E RCSB Protein Data Bank: TUT4 with bound GTP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0G RCSB Protein Data Bank: TUT4 with bound UpU]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Sandbox_Reserved_329&diff=1224629 Sandbox Reserved 329 2011-04-04T01:24:47Z

<p>Jessica Lowry: </p> <hr /> <div><br /> {{Template:Sandbox_Reserved_BCMB307}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[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.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites that cause diseases in humans such as African Sleeping Sickness. It has been suggested that the knowledge of TUTases may aid in the treatment of these diseases as TUTases function in RNA editing in these parasites, and thus can serve as enzymes to target.<ref name="second reference">PMID:11893335</ref> More specifically TUT4 catalyzes a reaction that adds a nucleotide, from a nucleotide triphosphate, to uridine monophosphate (UMP), the minimally required terminal RNA substrate.<ref name="primary citation">PMID:17785418</ref> TUTase4 is able to bind to the nucleotide triphosphates ATP, CTP, GTP or UTP, however, UTP and CTP are preferred, whereas ATP and GTP [[ligand]]s have been shown to cause a significant decrease in enzymatic activity.<ref name="primary citation">PMID:17785418</ref> The preference for UTP causes TUTase4 to typically add a uracil nucleotide to the RNA substrate. This selectivity has a variety of mechanisms, including a loss of coplanarity (π-electron stacking) between the ATP and a tyrosine of the active site (Y189) required for catalysis, and reduced stacking between the UMP and ATP rings.<ref name="primary citation">PMID:17785418</ref> The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg<sup>2+</sup> ions required by the ligand.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> 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&nbsp;[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><br /> <br /> [[Image:Signature_Motif.jpg|thumb|left|upright=2.0|Signature motif of the polymerase β<br /> nucleotidyltransferase superfamily, as shown (green) in TUT4 with bound ATP.]]<br /> <br /> == TRANSFERASE REACTION ==<br /> <br /> 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><br /> <br /> <br /> <br /> <br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank: TUT4 with bound ATP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0C RCSB Protein Data Bank: TUT4 with bound CTP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0F RCSB Protein Data Bank: TUT4 with bound UTP and UMP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0E RCSB Protein Data Bank: TUT4 with bound GTP]<br /> <br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0G RCSB Protein Data Bank: TUT4 with bound UpU]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Sandbox_Reserved_329&diff=1224628 Sandbox Reserved 329 2011-04-04T01:23:40Z

<p>Jessica Lowry: </p> <hr /> <div><br /> {{Template:Sandbox_Reserved_BCMB307}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[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.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites that cause diseases in humans such as African Sleeping Sickness. It has been suggested that the knowledge of TUTases may aid in the treatment of these diseases as TUTases function in RNA editing in these parasites, and thus can serve as enzymes to target.<ref name="second reference">PMID:11893335</ref> More specifically TUT4 catalyzes a reaction that adds a nucleotide, from a nucleotide triphosphate, to uridine monophosphate (UMP), the minimally required terminal RNA substrate.<ref name="primary citation">PMID:17785418</ref> TUTase4 is able to bind to the nucleotide triphosphates ATP, CTP, GTP or UTP, however, UTP and CTP are preferred, whereas ATP and GTP [[ligand]]s have been shown to cause a significant decrease in enzymatic activity.<ref name="primary citation">PMID:17785418</ref> The preference for UTP causes TUTase4 to typically add a uracil nucleotide to the RNA substrate. This selectivity has a variety of mechanisms, including a loss of coplanarity (π-electron stacking) between the ATP and a tyrosine of the active site (Y189) required for catalysis, and reduced stacking between the UMP and ATP rings.<ref name="primary citation">PMID:17785418</ref> The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg<sup>2+</sup> ions required by the ligand.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> 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&nbsp;[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><br /> <br /> [[Image:Signature_Motif.jpg|thumb|left|upright=2.0|Signature motif of the polymerase β<br /> nucleotidyltransferase superfamily, as shown (green) in TUT4 with bound ATP.]]<br /> <br /> == TRANSFERASE REACTION ==<br /> <br /> 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><br /> <br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank: TUT4 with bound ATP]<br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0C RCSB Protein Data Bank: TUT4 with bound CTP]<br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0F RCSB Protein Data Bank: TUT4 with bound UTP and UMP]<br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0E RCSB Protein Data Bank: TUT4 with bound GTP]<br /> [http://www.rcsb.org/pdb/explore.do?structureId=2Q0G RCSB Protein Data Bank: TUT4 with bound UpU]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Sandbox_Reserved_329&diff=1224614 Sandbox Reserved 329 2011-04-04T01:11:54Z

<p>Jessica Lowry: </p> <hr /> <div><br /> {{Template:Sandbox_Reserved_BCMB307}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[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.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites that cause diseases in humans such as African Sleeping Sickness. It has been suggested that the knowledge of TUTases may aid in the treatment of these diseases as TUTases function in RNA editing in these parasites, and thus can serve as enzymes to target.<ref name="second reference">PMID:11893335</ref> More specifically TUT4 catalyzes a reaction that adds a nucleotide, from a nucleotide triphosphate, to uridine monophosphate (UMP), the minimally required terminal RNA substrate.<ref name="primary citation">PMID:17785418</ref> TUTase4 is able to bind to the nucleotide triphosphates ATP, CTP, GTP or UTP, however, UTP and CTP are preferred, whereas ATP and GTP [[ligand]]s have been shown to cause a significant decrease in enzymatic activity.<ref name="primary citation">PMID:17785418</ref> The preference for UTP causes TUTase4 to typically add a uracil nucleotide to the RNA substrate. This selectivity has a variety of mechanisms, including a loss of coplanarity (π-electron stacking) between the ATP and a tyrosine of the active site (Y189) required for catalysis, and reduced stacking between the UMP and ATP rings.<ref name="primary citation">PMID:17785418</ref> The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg<sup>2+</sup> ions required by the ligand.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> 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&nbsp;[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><br /> <br /> [[Image:Signature_Motif.jpg|thumb|left|upright=2.0|Signature motif of the polymerase β<br /> nucleotidyltransferase superfamily, as shown (green) in TUT4 with bound ATP.]]<br /> <br /> == TRANSFERASE REACTION ==<br /> <br /> 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><br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Sandbox_Reserved_329&diff=1224612 Sandbox Reserved 329 2011-04-04T01:07:30Z

<p>Jessica Lowry: </p> <hr /> <div><br /> {{Template:Sandbox_Reserved_BCMB307}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[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.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites that cause diseases in humans such as African Sleeping Sickness. It has been suggested that the knowledge of TUTases may aid in the treatment of these diseases as TUTases function in RNA editing in these parasites, and thus can serve as enzymes to target.<ref name="second reference">PMID:11893335</ref> More specifically TUT4 catalyzes a reaction that adds a nucleotide, from a nucleotide triphosphate, to uridine monophosphate (UMP), the minimally required terminal RNA substrate.<ref name="primary citation">PMID:17785418</ref> TUTase4 is able to bind to the nucleotide triphosphates ATP, CTP, GTP or UTP, however, UTP and CTP are preferred, whereas ATP and GTP [[ligand]]s have been shown to cause a significant decrease in enzymatic activity.<ref name="primary citation">PMID:17785418</ref> The preference for UTP causes TUTase4 to typically add a uracil nucleotide to the RNA substrate. This selectivity has a variety of mechanisms, including a loss of coplanarity (π-electron stacking) between the ATP and a tyrosine of the active site (Y189) required for catalysis, and reduced stacking between the UMP and ATP rings.<ref name="primary citation">PMID:17785418</ref> The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg<sup>2+</sup> ions required by the ligand.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> 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><br /> <br /> [[Image:Signature_Motif.jpg|thumb|left|upright=2.0|Signature motif of the polymerase β<br /> nucleotidyltransferase superfamily, as shown (green) in TUT4 with bound ATP.]]<br /> <br /> == TRANSFERASE REACTION ==<br /> <br /> 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><br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Sandbox_Reserved_329&diff=1224607 Sandbox Reserved 329 2011-04-04T01:00:48Z

<p>Jessica Lowry: </p> <hr /> <div><br /> {{Template:Sandbox_Reserved_BCMB307}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[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.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites that cause diseases in humans such as African Sleeping Sickness. It has been suggested that the knowledge of TUTases may aid in the treatment of these diseases as TUTases function in RNA editing in these parasites, and thus can serve as enzymes to target.<ref>PMID:11893335</ref> More specifically TUT4 catalyzes a reaction that adds a nucleotide, from a nucleotide triphosphate, to uridine monophosphate (UMP), the minimally required terminal RNA substrate.<ref name="primary citation">PMID:17785418</ref> TUTase4 is able to bind to the nucleotide triphosphates ATP, CTP, GTP or UTP, however, UTP and CTP are preferred, whereas ATP and GTP [[ligand]]s have been shown to cause a significant decrease in enzymatic activity.<ref name="primary citation">PMID:17785418</ref> The preference for UTP causes TUTase4 to typically add a uracil nucleotide to the RNA substrate. This selectivity has a variety of mechanisms, including a loss of coplanarity (π-electron stacking) between the ATP and a tyrosine of the active site (Y189) required for catalysis, and reduced stacking between the UMP and ATP rings.<ref name="primary citation">PMID:17785418</ref> The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg<sup>2+</sup> ions required by the ligand.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> 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><br /> <br /> [[Image:Signature_Motif.jpg|thumb|left|upright=2.0|Signature motif of the polymerase β<br /> nucleotidyltransferase superfamily, as shown (green) in TUT4 with bound ATP.]]<br /> <br /> == TRANSFERASE REACTION ==<br /> <br /> 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><br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Sandbox_Reserved_329&diff=1224605 Sandbox Reserved 329 2011-04-04T00:59:15Z

<p>Jessica Lowry: </p> <hr /> <div><br /> {{Template:Sandbox_Reserved_BCMB307}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[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.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites that cause diseases in humans such as African Sleeping Sickness. It has been suggested that the knowledge of TUTases may aid in the treatment of these diseases as TUTases function in RNA editing in these parasites, and thus can serve as enzymes to target.<ref>PMID:11893335</ref> More specifically TUT4 catalyzes a reaction that adds a nucleotide, from a nucleotide triphosphate, to uridine monophosphate (UMP), the minimally required terminal RNA substrate.<ref name="primary citation">PMID:17785418</ref> TUTase4 is able to bind to the nucleotide triphosphates ATP, CTP, GTP or UTP, however, UTP and CTP are preferred, whereas ATP and GTP [[ligand]]s have been shown to cause a significant decrease in enzymatic activity.<ref name="primary citation">PMID:17785418</ref> The preference for UTP causes TUTase4 to typically add a uracil nucleotide to the RNA substrate. This selectivity has a variety of mechanisms, including a loss of coplanarity (π-electron stacking) between the ATP and a tyrosine of the active site (Y189) required for catalysis, and reduced stacking between the UMP and ATP rings.<ref name="primary citation">PMID:17785418</ref> The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg<sup>2+</sup> ions required by the ligand.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> 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><br /> <br /> [[Image:Signature_Motif.jpg|thumb|left|upright=2.0|Signature motif of the polymerase β �<br /> nucleotidyltransferase superfamily, as shown (in green) in TUT4 with bound ATP.]]<br /> <br /> == TRANSFERASE REACTION ==<br /> <br /> 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><br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=File:Signature_Motif.jpg&diff=1224602 File:Signature Motif.jpg 2011-04-04T00:53:46Z

<p>Jessica Lowry: </p> <hr /> <div>== Licensing ==<br /> {{PD-self}}</div>

Jessica Lowry https://proteopedia.org/index.php?title=Sandbox_Reserved_329&diff=1224600 Sandbox Reserved 329 2011-04-04T00:47:51Z

<p>Jessica Lowry: </p> <hr /> <div><br /> {{Template:Sandbox_Reserved_BCMB307}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|alt=Secondary Structure Succession of ATP-bound TUTases. Secondary structure residues are ordered from blue to red.|Secondary structure succession of TUT4 with bound ATP.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites that cause diseases in humans such as African Sleeping Sickness. It has been suggested that the knowledge of TUTases may aid in the treatment of these diseases as TUTases function in RNA editing in these parasites, and thus can serve as enzymes to target.<ref>PMID:11893335</ref> More specifically TUT4 catalyzes a reaction that adds a nucleotide, from a nucleotide triphosphate, to uridine monophosphate (UMP), the minimally required terminal RNA substrate.<ref name="primary citation">PMID:17785418</ref> TUTase4 is able to bind to the nucleotide triphosphates ATP, CTP, GTP or UTP, however, UTP and CTP are preferred, whereas ATP and GTP [[ligand]]s have been shown to cause a significant decrease in enzymatic activity.<ref name="primary citation">PMID:17785418</ref> The preference for UTP causes TUTase4 to typically add a uracil nucleotide to the RNA substrate. This selectivity has a variety of mechanisms, including a loss of coplanarity (π-electron stacking) between the ATP and a tyrosine of the active site (Y189) required for catalysis, and reduced stacking between the UMP and ATP rings.<ref name="primary citation">PMID:17785418</ref> The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg<sup>2+</sup> ions required by the ligand.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> 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><br /> <br /> == TRANSFERASE REACTION ==<br /> <br /> 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><br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Sandbox_Reserved_329&diff=1224529 Sandbox Reserved 329 2011-04-03T23:21:08Z

<p>Jessica Lowry: </p> <hr /> <div><br /> {{Template:Sandbox_Reserved_BCMB307}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|alt=Secondary Structure Succession of ATP-bound TUTases. Secondary structure residues are ordered from blue to red.|Secondary structure succession of TUT4 with bound ATP.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites that cause diseases in humans such as African Sleeping Sickness. It has been suggested that the knowledge of TUTases may aid in the treatment of these diseases as TUTases function in RNA editing in these parasites, and thus can serve as enzymes to target.<ref>PMID:11893335</ref> More specifically TUT4 catalyzes a reaction that adds a nucleotide, from a nucleotide triphosphate, to uridine monophosphate (UMP), the minimally required terminal RNA substrate.<ref name="primary citation">PMID:17785418</ref> TUTase4 is able to bind to the nucleotide triphosphates ATP, CTP, GTP or UTP, however, UTP and CTP are preferred, whereas ATP and GTP [[ligand]]s have been shown to cause a significant decrease in enzymatic activity.<ref name="primary citation">PMID:17785418</ref> The preference for UTP causes TUTase4 to typically add a uracil nucleotide to the RNA substrate. This selectivity has a variety of mechanisms, including a loss of coplanarity (π-electron stacking) between the ATP and a tyrosine of the active site (Y189) required for catalysis, and reduced stacking between the UMP and ATP rings.<ref name="primary citation">PMID:17785418</ref> The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg<sup>2+</sup> ions required by the ligand.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> 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 <scene name='Sandbox_Reserved_329/Hydrophobic_hbond_interactions/1'>interactions</scene> 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 R121, D68, and D136 of TUT4 with the RNA substrate, and among S148, Y189, and N147 of the apo protein with the ATP complex.<ref name="primary citation">PMID:17785418</ref> Hydrophobic interactions with the RNA substrate and V122 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><br /> <br /> == TRANSFERASE REACTION ==<br /> <br /> 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><br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Sandbox_Reserved_329&diff=1224238 Sandbox Reserved 329 2011-04-03T03:46:11Z

<p>Jessica Lowry: </p> <hr /> <div><br /> {{Template:Sandbox_Reserved_BCMB307}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|alt=Secondary Structure Succession of ATP-bound TUTases. Secondary structure residues are ordered from blue to red.|Secondary structure succession of TUT4 with bound ATP.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites that cause diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> TUTases can function in RNA editing; more specifically TUT4 catalyzes a reaction that adds a nucleotide, from a nucleotide triphosphate, to uridine monophosphate (UMP), the minimally required terminal RNA substrate.<ref name="primary citation">PMID:17785418</ref> TUTase4 is able to bind to the nucleotide triphosphates ATP, CTP, GTP or UTP, however, UTP and CTP are preferred, whereas ATP and GTP [[ligand]]s have been shown to cause a significant decrease in enzymatic activity.<ref name="primary citation">PMID:17785418</ref> The preference for UTP causes TUTase4 to typically add a uracil nucleotide to the RNA substrate. This selectivity has a variety of mechanisms, including a loss of coplanarity (π-electron stacking) between the ATP and a tyrosine of the active site (Y189) required for catalysis, and reduced stacking between the UMP and ATP rings.<ref name="primary citation">PMID:17785418</ref> The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg<sup>2+</sup> ions required by the ligand.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> 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 tyrosine (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. 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. Hydrogen bonding 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 R121, D68, and D136 of TUT4 with the RNA substrate, and among S148, Y189, and N147 of the apo protein with the ATP complex. Hydrophobic interactions with the RNA substrate and V122 of TUT4 also contribute to the transferase reaction. 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 to, <ref name="primary citation">PMID:17785418</ref> Thus, these <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are vital in catalyzing this reaction. <scene name='Sandbox_Reserved_329/Tyr189/1'>tyrosine residue</scene><br /> <scene name='Sandbox_Reserved_329/Hydrophobic_hbond_interactions/1'>interactions</scene><br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Sandbox_Reserved_329&diff=1224222 Sandbox Reserved 329 2011-04-03T03:08:37Z

<p>Jessica Lowry: </p> <hr /> <div><br /> {{Template:Sandbox_Reserved_BCMB307}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|alt=Secondary Structure Succession of ATP-bound TUTases. Secondary structure residues are ordered from blue to red.|Secondary structure succession of TUT4 with bound ATP.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites that cause diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> TUTases can function in RNA editing; more specifically TUT4 catalyzes a reaction that adds a nucleotide, from a nucleotide triphosphate, to uridine monophosphate (UMP), the minimally required terminal RNA substrate.<ref name="primary citation">PMID:17785418</ref> TUTase4 is able to bind to the nucleotide triphosphates ATP, CTP, GTP or UTP, however, UTP and CTP are preferred, whereas ATP and GTP [[ligands]] have been shown to cause a significant decrease in enzymatic activity.<ref name="primary citation">PMID:17785418</ref> The preference for UTP causes TUTase4 to typically add a uracil nucleotide to the RNA substrate. This selectivity has a variety of mechanisms, including a loss of coplanarity (π-electron stacking) between the ATP and a tyrosine of the active site (Y189) required for catalysis, and reduced stacking between the UMP and ATP rings.<ref name="primary citation">PMID:17785418</ref> The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg<sup>2+</sup> ions required by the ligand.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> 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 pi-electron stacking with both the active site tyrosine (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. The Mg2+ ions are coordinated by three aspartate residues (D66, D68, and D136) which are conserved among TUTases, and thus vital in the transferase reaction. Hydrogen bonding 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 R121, D68, and D136 of TUT4 with the RNA substrate, and among S148, Y189, and N147 of the apo protein with the ATP complex. Hydrophobic interactions with the RNA substrate and V122 of TUT4 also contribute to the transferase reaction. The lack of triple stacking as well as different hydrogen bonding interactions contribute to the preference for TUT4 towards UTP instead of ATP, however it is thought that minimal mutations would be required to, however many TUTases involved in RNA editing are shown to exhibit preference for binding to UTP instead.<ref name="primary citation">PMID:17785418</ref> Three <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are conserved in TUTases, and are required for coordinating the Mg<sup>2+</sup> ions in some TUTases. <ref name="primary citation">PMID:17785418</ref> Thus, these <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are vital in catalyzing this reaction. <scene name='Sandbox_Reserved_329/Tyr189/1'>tyrosine residue</scene><br /> <scene name='Sandbox_Reserved_329/Hydrophobic_hbond_interactions/1'>interactions</scene><br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Sandbox_Reserved_329&diff=1224081 Sandbox Reserved 329 2011-04-02T22:18:46Z

<p>Jessica Lowry: </p> <hr /> <div><br /> {{Template:Sandbox_Reserved_BCMB307}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|alt=Secondary Structure Succession of ATP-bound TUTases. Secondary structure residues are ordered from blue to red.|Secondary structure succession of TUT4 with bound ATP.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites that cause diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> TUTases can function in RNA editing; more specifically TUT4 catalyzes a reaction that adds a nucleotide, from a nucleotide triphosphate, to uridine monophosphate (UMP), the minimally required terminal RNA substrate.<ref name="primary citation">PMID:17785418</ref> TUTase4 is able to bind to the nucleotide triphosphates ATP, CTP, GTP or UTP, however, UTP and CTP are preferred, whereas ATP and GTP [[ligands]] have been shown to cause a significant decrease in enzymatic activity.<ref name="primary citation">PMID:17785418</ref> The preference for UTP causes TUTase4 to typically add a uracil nucleotide to the RNA substrate. This selectivity has a variety of mechanisms, including a loss of coplanarity (π-electron stacking) between the ATP and a tyrosine of the active site (Y189) required for catalysis, and reduced stacking between the UMP and ATP rings.<ref name="primary citation">PMID:17785418</ref> The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg<sup>2+</sup> ions required by the ligand.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> TUT4 with bound ATP <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions, however many TUTases involved in RNA editing are shown to exhibit preference for binding to UTP instead.<ref name="primary citation">PMID:17785418</ref> Three <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are conserved in TUTases, and are required for coordinating the Mg<sup>2+</sup> ions in some TUTases. <ref name="primary citation">PMID:17785418</ref> Thus, these <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are vital in catalyzing this reaction. <scene name='Sandbox_Reserved_329/Tyr189/1'>tyrosine residue</scene><br /> <scene name='Sandbox_Reserved_329/Hydrophobic_hbond_interactions/1'>interactions</scene><br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Sandbox_Reserved_329&diff=1224054 Sandbox Reserved 329 2011-04-02T20:54:44Z

<p>Jessica Lowry: </p> <hr /> <div><br /> {{Template:Sandbox_Reserved_BCMB307}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|alt=Secondary Structure Succession of ATP-bound TUTases. Secondary structure residues are ordered from blue to red.|Secondary structure succession of ATP-bound TUTases.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites that cause diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> TUTases can function in RNA editing; more specifically TUTase4 catalyzes a reaction that adds a nucleotide, from a nucleotide triphosphate, to uridine monophosphate (UMP), the minimally required terminal RNA substrate.<ref name="primary citation">PMID:17785418</ref> TUTase4 is able to bind to the nucleotide triphosphates ATP, CTP, GTP or UTP, however, UTP and CTP are preferred, whereas ATP and GTP ligands have been shown to cause a significant decrease in enzymatic activity.<ref name="primary citation">PMID:17785418</ref> The preference for UTP causes TUTase4 to typically add a uracil nucleotide to the RNA substrate. This selectivity has a variety of mechanisms, including a loss of coplanarity (pi-electron stacking) between the ATP and a tyrosine of the active site (Y189) required for catalysis, and reduced stacking between the UMP and ATP rings.<ref name="primary citation">PMID:17785418</ref> The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg<sup>2+</sup> ions required by the ligand.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> The uridylyl transferase bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions, however many TUTases involved in RNA editing are shown to exhibit preference for binding to UTP instead.<ref name="primary citation">PMID:17785418</ref> Three <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are conserved in TUTases, and are required for coordinating the Mg<sup>2+</sup> ions in some TUTases. <ref name="primary citation">PMID:17785418</ref> Thus, these <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are vital in catalyzing this reaction. <scene name='Sandbox_Reserved_329/Tyr189/1'>tyrosine residue</scene><br /> <scene name='Sandbox_Reserved_329/Hydrophobic_hbond_interactions/1'>interactions</scene><br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Sandbox_Reserved_329&diff=1224053 Sandbox Reserved 329 2011-04-02T20:52:18Z

<p>Jessica Lowry: </p> <hr /> <div><br /> {{Template:Sandbox_Reserved_BCMB307}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|alt=Secondary Structure Succession of ATP-bound TUTases. Secondary structure residues are ordered from blue to red.|Secondary structure succession of ATP-bound TUTases.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites that cause diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> TUTases can function in RNA editing; more specifically TUTase4 catalyzes a reaction that adds a nucleotide, from a nucleotide triphosphate, to uridine monophosphate (UMP), the minimally required terminal RNA substrate. (ref) TUTase4 is able to bind to the nucleotide triphosphates ATP, CTP, GTP or UTP, however, UTP and CTP are preferred, whereas ATP and GTP ligands have been shown to cause a significant decrease in enzymatic activity (ref). The preference for UTP causes TUTase4 to typically add a uracil nucleotide to the RNA substrate. This selectivity has a variety of mechanisms, including a loss of coplanarity (pi-electron stacking) between the ATP and a tyrosine of the active site (Y189) required for catalysis, and reduced stacking between the UMP and ATP rings. The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg<sup>2+</sup> ions required by the ligand.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> The uridylyl transferase bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions, however many TUTases involved in RNA editing are shown to exhibit preference for binding to UTP instead.<ref name="primary citation">PMID:17785418</ref> Three <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are conserved in TUTases, and are required for coordinating the Mg<sup>2+</sup> ions in some TUTases. <ref name="primary citation">PMID:17785418</ref> Thus, these <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are vital in catalyzing this reaction. <scene name='Sandbox_Reserved_329/Tyr189/1'>tyrosine residue</scene><br /> <scene name='Sandbox_Reserved_329/Hydrophobic_hbond_interactions/1'>interactions</scene><br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Sandbox_Reserved_329&diff=1222707 Sandbox Reserved 329 2011-03-30T23:43:46Z

<p>Jessica Lowry: </p> <hr /> <div><br /> {{Template:Sandbox_Reserved_BCMB307}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|alt=Secondary Structure Succession of ATP-bound TUTases. Secondary structure residues are ordered from blue to red.|Secondary structure succession of ATP-bound TUTases.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites causing diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> TUTases can function in RNA editing; more specifically TUTase4 catalyzes a reaction that adds a uridine monophosphate (UMP) from UTP to a RNA substrate. Trypanosomal TUTases have RNA substrates that are shown to select for cognate nucleosides and provide a metal ion binding site for Mg<sup>2+</sup> ions.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> The uridylyl transferase bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions, however many TUTases involved in RNA editing are shown to exhibit preference for binding to UTP instead.<ref name="primary citation">PMID:17785418</ref> Three <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are conserved in TUTases, and are required for coordinating the Mg<sup>2+</sup> ions in some TUTases. <ref name="primary citation">PMID:17785418</ref> Thus, these <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are vital in catalyzing this reaction. <scene name='Sandbox_Reserved_329/Tyr189/1'>tyrosine residue</scene><br /> <scene name='Sandbox_Reserved_329/Hydrophobic_hbond_interactions/1'>interactions</scene><br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Sandbox_Reserved_329&diff=1220392 Sandbox Reserved 329 2011-03-29T21:28:21Z

<p>Jessica Lowry: </p> <hr /> <div><br /> {{Template:Sandbox_Reserved_BCMB307}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|alt=Secondary Structure Succession of ATP-bound TUTases. Secondary structure residues are ordered from blue to red.|Secondary structure succession of ATP-bound TUTases.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites causing diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> TUTases function in RNA editing; more specifically they catalyze the reaction that adds UMP to a RNA substrate. Trypanosomal TUTases have RNA substrates that are shown to select for cognate nucleosides and provide a metal ion binding site for Mg<sup>2+</sup> ions.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> The uridylyl transferase bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions, however many TUTases involved in RNA editing are shown to exhibit preference for binding to UTP instead.<ref name="primary citation">PMID:17785418</ref> Three <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are conserved in TUTases, and are required for coordinating the Mg<sup>2+</sup> ions in some TUTases. <ref name="primary citation">PMID:17785418</ref> Thus, these <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are vital in catalyzing this reaction. <scene name='Sandbox_Reserved_329/Tyr189/1'>tyrosine residue</scene><br /> <scene name='Sandbox_Reserved_329/Hydrophobic_hbond_interactions/1'>interactions</scene><br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Sandbox_Reserved_329&diff=1220354 Sandbox Reserved 329 2011-03-29T18:51:36Z

<p>Jessica Lowry: </p> <hr /> <div><br /> {{Template:Sandbox_Reserved_BCMB307}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|alt=Secondary Structure Succession of ATP-bound TUTases. Secondary structure residues are ordered from blue to red.|Secondary structure succession of ATP-bound TUTases.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites causing diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> TUTases function in RNA editing; more specifically they catalyze the reaction that adds UMP to a RNA substrate. Trypanosomal TUTases have RNA substrates that are shown to select for cognate nucleosides and provide a metal ion binding site for Mg<sup>2+</sup> ions.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> The uridylyl transferase bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions, however many TUTases involved in RNA editing are shown to exhibit preference for binding to UTP instead.<ref name="primary citation">PMID:17785418</ref> Three <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are conserved in TUTases, and are required for coordinating the Mg<sup>2+</sup> ions in some TUTases. <ref name="primary citation">PMID:17785418</ref> Thus, these <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are vital in catalyzing this reaction. <scene name='Sandbox_Reserved_329/Tyr189/1'>tyrosine residue</scene><br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Sandbox_Reserved_329&diff=1216658 Sandbox Reserved 329 2011-03-22T00:35:15Z

<p>Jessica Lowry: </p> <hr /> <div><br /> {{Template:Sandbox_Reserved_BCMB307}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|alt=Secondary Structure Succession of ATP-bound TUTases. Secondary structure residues are ordered from blue to red.|Secondary structure succession of ATP-bound TUTases.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites causing diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> TUTases function in RNA editing; more specifically they catalyze the reaction that adds UMP to a RNA substrate. Trypanosomal TUTases have RNA substrates that are shown to select for cognate nucleosides and provide a metal ion binding site for Mg<sup>2+</sup> ions.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> The uridylyl transferase bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions, however many TUTases involved in RNA editing are shown to exhibit preference for binding to UTP instead.<ref name="primary citation">PMID:17785418</ref> Three <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are conserved in TUTases, and are required for coordinating the Mg<sup>2+</sup> ions in some TUTases. <ref name="primary citation">PMID:17785418</ref> Thus, these <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are vital in catalyzing this reaction.<br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Reserved_Sandbox_329&diff=1216168 Reserved Sandbox 329 2011-03-16T23:28:28Z

<p>Jessica Lowry: </p> <hr /> <div>== '''Uridylyl transferases''' ==<br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|alt=Secondary Structure Succession of ATP-bound TUTases. Secondary structure residues are ordered from blue to red.|Secondary structure succession of ATP-bound TUTases.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites causing diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> TUTases function in RNA editing; more specifically they catalyze the reaction that adds UMP to a RNA substrate. Trypanosomal TUTases have RNA substrates that are shown to select for cognate nucleosides and provide a metal ion binding site for Mg<sup>2+</sup> ions.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> The uridylyl transferase bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions, however many TUTases involved in RNA editing are shown to exhibit preference for binding to UTP instead.<ref name="primary citation">PMID:17785418</ref> Three <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are conserved in TUTases, and are required for coordinating the Mg<sup>2+</sup> ions in some TUTases. <ref name="primary citation">PMID:17785418</ref> Thus, these <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are vital in catalyzing this reaction.<br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Reserved_Sandbox_329&diff=1216167 Reserved Sandbox 329 2011-03-16T23:26:51Z

<p>Jessica Lowry: </p> <hr /> <div>== '''Uridylyl transferases''' ==<br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|alt=Secondary Structure Succession of ATP-bound TUTases. Secondary structure residues are ordered from blue to red.|Secondary structure succession of ATP-bound TUTases.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites causing diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> TUTases function in RNA editing; more specifically they catalyze the reaction that adds UMP to a RNA substrate. Trypanosomal TUTases have RNA substrates that are shown to select for cognate nucleosides and provide a metal ion binding site for Mg<sup>2+</sup> ions.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> The uridylyl transferase bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions, however many TUTases involved in RNA editing are shown to exhibit preference for binding to UTP instead.<ref name="primary citation">PMID:17785418</ref> Three <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are conserved in TUTases, and are required for coordinating the Mg<sup>2+</sup> ions in some TUTases. <ref name="primary citation">PMID:17785418</ref> Thus, these <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are vital in catalysing this reaction.<br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Reserved_Sandbox_329&diff=1216166 Reserved Sandbox 329 2011-03-16T23:20:52Z

<p>Jessica Lowry: </p> <hr /> <div>== '''Uridylyl transferases''' ==<br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|alt=Secondary Structure Succession of ATP-bound TUTases|Secondary structure succession of ATP-bound TUTases.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites causing diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> TUTases function in RNA editing; more specifically they catalyze the reaction that adds UMP to a RNA substrate. Trypanosomal TUTases have RNA substrates that are shown to select for cognate nucleosides and provide a metal ion binding site for Mg<sup>2+</sup> ions.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> The uridylyl transferase bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions, however many TUTases involved in RNA editing are shown to exhibit preference for binding to UTP instead.<ref name="primary citation">PMID:17785418</ref> Three <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are conserved in TUTases, and are required for coordinating the Mg<sup>2+</sup> ions in some TUTases. <ref name="primary citation">PMID:17785418</ref> Thus, these <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are vital in catalysing this reaction.<br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Reserved_Sandbox_329&diff=1216165 Reserved Sandbox 329 2011-03-16T23:20:08Z

<p>Jessica Lowry: </p> <hr /> <div>== '''Uridylyl transferases''' ==<br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|alt=Secondary Structure Succession of ATP-bound TUTases|Secondary structure succession of ATP-bound TUTases.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites causing diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> TUTases function in RNA editing; more specifically they catalyze the reaction that adds UMP to a RNA substrate. Trypanosomal TUTases have RNA substrates that are shown to select for cognate nucleosides and provide a metal ion binding site for Mg<sup>2+</sup> ions.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> The uridylyl transferase bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions, however many TUTases involved in RNA editing are shown to exhibit preference for binding to UTP instead.<ref name="primary citation">PMID:17785418</ref><br /> <br /> Three <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are conserved in TUTases, and are required for coordinating the Mg<sup>2+</sup> ions in some TUTases. <ref name="primary citation">PMID:17785418</ref> Thus, these <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are vital in catalysing this reaction.<br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Reserved_Sandbox_329&diff=1216147 Reserved Sandbox 329 2011-03-16T21:22:40Z

<p>Jessica Lowry: </p> <hr /> <div>== '''Uridylyl transferases''' ==<br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|alt=Secondary Structure Succession of ATP-bound TUTases|Secondary structure succession of ATP-bound TUTases.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites causing diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> TUTases function in RNA editing; more specifically they catalyze the reaction adding UMP to a RNA substrate. Trypanosomal TUTases have RNA substrates that are shown to select for cognate nucleosides and provide a metal ion binding site for Mg<sup>2+</sup> ions.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> The bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions.<br /> <br /> Three <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are conserved in TUTases, and are required for coordinating the Mg<sup>2+</sup> ions in some TUTases. <ref name="primary citation">PMID:17785418</ref><br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Reserved_Sandbox_329&diff=1216146 Reserved Sandbox 329 2011-03-16T21:20:41Z

<p>Jessica Lowry: </p> <hr /> <div>== '''Uridylyl transferases''' ==<br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|alt=Secondary Structure Succession of ATP-bound TUTases|Secondary structure succession of ATP-bound TUTases.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites causing diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> TUTases function in RNA editing; more specifically they catalyze the reaction adding UMP to a RNA substrate. Trypanosomal TUTases have RNA substrates that are shown to select for cognate nucleosides and provide a metal ion binding site for Mg<sup>2+</sup> ions. TUTases function in RNA editing; they add UMP to the 3' hydroxyl group.<ref name="primary citation">PMID:17785418</ref><br /> <br /> {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == STRUCTURE ==<br /> <br /> The bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions.<br /> <br /> Three <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are conserved in TUTases, and are required for coordinating the Mg<sup>2+</sup> ions in some TUTases. <ref name="primary citation">PMID:17785418</ref><br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Reserved_Sandbox_329&diff=1216142 Reserved Sandbox 329 2011-03-16T21:17:05Z

<p>Jessica Lowry: </p> <hr /> <div>{{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|alt=Secondary Structure Succession of ATP-bound TUTases|Secondary structure succession of ATP-bound TUTases.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites causing diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> TUTases function in RNA editing; more specifically they catalyze the reaction adding UMP to a RNA substrate. Trypanosomal TUTases have RNA substrates that are shown to select for cognate nucleosides and provide a metal ion binding site for Mg<sup>2+</sup> ions. TUTases function in RNA editing; they add UMP to the 3' hydroxyl group.<ref name="primary citation">PMID:17785418</ref><br /> <br /> == STRUCTURE ==<br /> <br /> The bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions.<br /> <br /> Three <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene> are conserved in TUTases, and are required for coordinating the Mg<sup>2+</sup> ions in some TUTases. <ref name="primary citation">PMID:17785418</ref><br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Reserved_Sandbox_329&diff=1216140 Reserved Sandbox 329 2011-03-16T21:10:43Z

<p>Jessica Lowry: </p> <hr /> <div>{{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|alt=Secondary Structure Succession of ATP-bound TUTases|Secondary structure succession of ATP-bound TUTases.]]<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites causing diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> TUTases function in RNA editing; more specifically they catalyze the reaction adding UMP to a RNA substrate. Trypanosomal TUTases have RNA substrates that are shown to select for cognate nucleosides and provide a metal ion binding site for Mg<sup>2+</sup> ions. TUTases function in RNA editing; they add UMP to the 3' hydroxyl group.<ref name="primary citation">PMID:17785418</ref><br /> <br /> == STRUCTURE ==<br /> <br /> The bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions.<br /> <br /> <scene name='Reserved_Sandbox_329/Asp/1'>aspartate residues</scene><br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Reserved_Sandbox_329&diff=1216116 Reserved Sandbox 329 2011-03-16T19:23:32Z

<p>Jessica Lowry: </p> <hr /> <div>{{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|alt=Secondary Structure Succession of ATP-bound TUTases|Secondary Structure Succession of ATP-bound TUTases.]]<br /> <br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites causing diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> Trypanosomal TUTases have RNA substrates that are shown to select for cognate nucleosides and provide a metal ion binding site for Mg<sup>2+</sup> ions. TUTases function in RNA editing; they add UMP to the 3' hydroxyl group.<ref name="primary citation">PMID:17785418</ref><br /> <br /> == STRUCTURE ==<br /> <br /> The bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions.<br /> <br /> <br /> <br /> ----<br /> <br /> <br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Reserved_Sandbox_329&diff=1216115 Reserved Sandbox 329 2011-03-16T19:20:38Z

<p>Jessica Lowry: </p> <hr /> <div>{{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites causing diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> Trypanosomal TUTases have RNA substrates that are shown to select for cognate nucleosides and provide a metal ion binding site for Mg<sup>2+</sup> ions. TUTases function in RNA editing; they add UMP to the 3' hydroxyl group.<ref name="primary citation">PMID:17785418</ref><br /> <br /> == STRUCTURE ==<br /> <br /> The bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions.<br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|alt=Secondary Structure Succession of ATP-bound TUTases|Secondary Structure Succession of ATP-bound TUTases.]]<br /> <br /> <br /> ----<br /> <br /> <br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Reserved_Sandbox_329&diff=1216113 Reserved Sandbox 329 2011-03-16T19:18:21Z

<p>Jessica Lowry: </p> <hr /> <div>{{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites causing diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> Trypanosomal TUTases have RNA substrates that are shown to select for cognate nucleosides and provide a metal ion binding site for Mg<sup>2+</sup> ions. TUTases function in RNA editing; they add UMP to the 3' hydroxyl group.<ref name="primary citation">PMID:17785418</ref><br /> <br /> == STRUCTURE ==<br /> <br /> The bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions.<br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|left|upright=2.0|alt=Secondary Structure Succession of ATP-bound TUTases|Secondary Structure Succession of ATP-bound TUTases.]]<br /> <br /> <br /> <br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Reserved_Sandbox_329&diff=1216112 Reserved Sandbox 329 2011-03-16T19:15:00Z

<p>Jessica Lowry: </p> <hr /> <div>{{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites causing diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> Trypanosomal TUTases have RNA substrates that are shown to select for cognate nucleosides and provide a metal ion binding site for Mg<sup>2+</sup> ions. TUTases function in RNA editing; they add UMP to the 3' hydroxyl group.<ref name="primary citation">PMID:17785418</ref><br /> <br /> == STRUCTURE ==<br /> <br /> The bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions.<br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|thumb|center|upright=2.0|alt=Secondary Structure Succession of ATP-bound TUTases|Secondary Structure Succession of ATP-bound TUTases.]]<br /> <br /> <br /> <br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=File:SECONDARY_STRUCTURE_SUCCESSION.jpg&diff=1216111 File:SECONDARY STRUCTURE SUCCESSION.jpg 2011-03-16T19:11:08Z

<p>Jessica Lowry: uploaded a new version of "Image:SECONDARY STRUCTURE SUCCESSION.jpg"</p> <hr /> <div>== Licensing ==<br /> {{PD-self}}</div>

Jessica Lowry https://proteopedia.org/index.php?title=Reserved_Sandbox_329&diff=1216109 Reserved Sandbox 329 2011-03-16T19:07:34Z

<p>Jessica Lowry: </p> <hr /> <div>{{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites causing diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> Trypanosomal TUTases have RNA substrates that are shown to select for cognate nucleosides and provide a metal ion binding site for Mg<sup>2+</sup> ions. TUTases function in RNA editing; they add UMP to the 3' hydroxyl group.<ref name="primary citation">PMID:17785418</ref><br /> <br /> == STRUCTURE ==<br /> <br /> The bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions.<br /> <br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg|left|400px|Secondary Structure Succession of ATP-bound TUTases]]<br /> <br /> <br /> <br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Reserved_Sandbox_329&diff=1216108 Reserved Sandbox 329 2011-03-16T18:58:02Z

<p>Jessica Lowry: </p> <hr /> <div>{{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites causing diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> Trypanosomal TUTases have RNA substrates that are shown to select for cognate nucleosides and provide a metal ion binding site for Mg<sup>2+</sup> ions. TUTases function in RNA editing; they add UMP to the 3' hydroxyl group.<ref name="primary citation">PMID:17785418</ref><br /> <br /> == STRUCTURE ==<br /> <br /> The bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions.<br /> [[Image:SECONDARY_STRUCTURE_SUCCESSION.jpg]]<br /> <br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=File:SECONDARY_STRUCTURE_SUCCESSION.jpg&diff=1216107 File:SECONDARY STRUCTURE SUCCESSION.jpg 2011-03-16T18:56:31Z

<p>Jessica Lowry: </p> <hr /> <div>== Licensing ==<br /> {{PD-self}}</div>

Jessica Lowry https://proteopedia.org/index.php?title=Reserved_Sandbox_329&diff=1216106 Reserved Sandbox 329 2011-03-16T17:49:31Z

<p>Jessica Lowry: </p> <hr /> <div>{{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites causing diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> Trypanosomal TUTases have RNA substrates that are shown to select for cognate nucleosides and provide a metal ion binding site for Mg<sup>2+</sup> ions. TUTases function in RNA editing; they add UMP to the 3' hydroxyl group.<ref name="primary citation">PMID:17785418</ref><br /> <br /> == STRUCTURE ==<br /> <br /> The bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions.<br /> <br /> <br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D RCSB Protein Data Bank]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Reserved_Sandbox_329&diff=1216105 Reserved Sandbox 329 2011-03-16T17:48:45Z

<p>Jessica Lowry: </p> <hr /> <div>{{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites causing diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> Trypanosomal TUTases have RNA substrates that are shown to select for cognate nucleosides and provide a metal ion binding site for Mg<sup>2+</sup> ions. TUTases function in RNA editing; they add UMP to the 3' hydroxyl group.<ref name="primary citation">PMID:17785418</ref><br /> <br /> == STRUCTURE ==<br /> <br /> The bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions.<br /> <br /> <br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> [[http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D/ RCSB Protein Data Bank]]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Reserved_Sandbox_329&diff=1216104 Reserved Sandbox 329 2011-03-16T17:45:19Z

<p>Jessica Lowry: </p> <hr /> <div>{{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania'' ssp, parasites causing diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> Trypanosomal TUTases have RNA substrates that are shown to select for cognate nucleosides and provide a metal ion binding site for Mg<sup>2+</sup> ions. TUTases function in RNA editing; they add UMP to the 3' hydroxyl group.<ref name="primary citation">PMID:17785418</ref><br /> <br /> == STRUCTURE ==<br /> <br /> The bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions.<br /> <br /> <br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> RCSB Protein Data Bank [[http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D]]</div>

Jessica Lowry https://proteopedia.org/index.php?title=Reserved_Sandbox_329&diff=1216103 Reserved Sandbox 329 2011-03-16T17:43:04Z

<p>Jessica Lowry: </p> <hr /> <div>{{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}}<br /> <br /> == '''Uridylyl transferases''' ==<br /> <br /> == INTRODUCTION ==<br /> <br /> Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.<ref name="primary citation">PMID:17785418</ref> TUTases have been isolated from ''Trypanosoma brucei'' and also ''Leishmania ssp'', parasites causing diseases in humans such as African Sleeping Sickness.<ref>PMID:11893335</ref> Trypanosomal TUTases have RNA substrates that are shown to select for cognate nucleosides and provide a metal ion binding site for Mg<sup>2+</sup> ions. TUTases function in RNA editing; they add UMP to the 3' hydroxyl group.<ref name="primary citation">PMID:17785418</ref><br /> <br /> == STRUCTURE ==<br /> <br /> The bound [[ligand]] is an <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> with two Mg<sup>2+</sup> ions.<br /> <br /> <br /> <br /> <br /> == REFERENCES ==<br /> <references/><br /> <br /> == External Links ==<br /> <br /> RCSB Protein Data Bank [[http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q0D]]</div>

Jessica Lowry