Sandbox Reserved 329
From Proteopedia
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== INTRODUCTION == | == INTRODUCTION == | ||
| - | 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 [[ | + | 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> |
{{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}} | {{STRUCTURE_2q0d | PDB=2q0d | SCENE=Reserved_Sandbox_329/Scene1/1}} | ||
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== STRUCTURE == | == STRUCTURE == | ||
| - | TUT4 with a bound <scene name='Reserved_Sandbox_329/Ligand/4'>ATP complex</scene> (consisting of an ATP molecule and two Mg<sup>2+</sup> ions) has little | + | 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> |
<scene name='Sandbox_Reserved_329/Hydrophobic_hbond_interactions/1'>interactions</scene> | <scene name='Sandbox_Reserved_329/Hydrophobic_hbond_interactions/1'>interactions</scene> | ||
Revision as of 03:46, 3 April 2011
| This Sandbox is Reserved from January 10, 2010, through April 10, 2011 for use in BCMB 307-Proteins course taught by Andrea Gorrell at the University of Northern British Columbia, Prince George, BC, Canada. |
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Contents |
Uridylyl transferases
INTRODUCTION
Terminal uridylyl transferases (TUTases) belong to a superfamily of polymerase ß nucleotidyl transferases.[1] TUTases have been isolated from Trypanosoma brucei and also Leishmania ssp, parasites that cause diseases in humans such as African Sleeping Sickness.[2] 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.[1] 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.[1] 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.[1] The RNA substrate in trypanosomal TUTases selects for cognate nucleosides and provides a metal ion binding site for Mg2+ ions required by the ligand.[1]
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| 2q0d, resolution 2.00Å () | |||||||||
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| Ligands: | , | ||||||||
| Gene: | TUT4 (Trypanosoma brucei) | ||||||||
| Activity: | RNA uridylyltransferase, with EC number 2.7.7.52 | ||||||||
| Related: | 2ikf, 2nom | ||||||||
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| Resources: | FirstGlance, OCA, RCSB, PDBsum | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
STRUCTURE
TUT4 with a bound (consisting of an ATP molecule and two Mg2+ 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 Mg2+ ions are coordinated by three (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, [1] Thus, these are vital in catalyzing this reaction.
REFERENCES
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5 Stagno J, Aphasizheva I, Aphasizhev R, Luecke H. Dual role of the RNA substrate in selectivity and catalysis by terminal uridylyl transferases. Proc Natl Acad Sci U S A. 2007 Sep 11;104(37):14634-9. Epub 2007 Sep 4. PMID:17785418
- ↑ Aphasizhev R, Sbicego S, Peris M, Jang SH, Aphasizheva I, Simpson AM, Rivlin A, Simpson L. Trypanosome mitochondrial 3' terminal uridylyl transferase (TUTase): the key enzyme in U-insertion/deletion RNA editing. Cell. 2002 Mar 8;108(5):637-48. PMID:11893335
