Sandbox 201: Difference between revisions
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'''T4 RNA ligase 1 (Rnl1)''' | |||
---- | |||
{{STRUCTURE_2c5u|right| PDB=2C5U | SIZE=300 | SCENE=}} | {{STRUCTURE_2c5u|right| PDB=2C5U | SIZE=300 | SCENE=}} | ||
[[Image:Overall_structure_of_T4_RNA_ligase.png|thumb|left|An overall structure of the T4 RNA ligase (Rnl1) with AMPcPP. Alpha-helices are colored in ''cyan''. The beta-strands are colored in ''red''. Loops are colored in ''purple''. The AMPcPP molecule is shown as a stick drawing in ''yellow''.]] | [[Image:Overall_structure_of_T4_RNA_ligase.png|thumb|left|An overall structure of the T4 RNA ligase (Rnl1) with AMPcPP. Alpha-helices are colored in ''cyan''. The beta-strands are colored in ''red''. Loops are colored in ''purple''. The AMPcPP molecule is shown as a stick drawing in ''yellow''.]] | ||
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Rnl1 is in fact a tRNA repair enzyme used by the T4 bacteriophage to escape hosts antiviral response. Enzyme functioning requires ATP and divalent metal ions. The T4 ligase repairs the tRNA<sup>Lys</sup> by joining its 5'-PO<sub>4</sub> and 3'-OH groups via series of three nucleotidyl transfer steps in a ping-pong enzymatic mechanism. First, the Lys<sup>99</sup> of the enzyme reacts with the a phosphorus of ATP and forms a covalent intermediate: ligase-(lysyl-N)-AMP. Pyrophosphate is also produced during this step. Secondly, AMP is transferred from the intermediate to the 5'- PO<sub>4</sub> terminus of a tRNA to form an tRNA-adenylate intermediate (AppRNA). Finally, the ligase catalyzes the attack of the 3'-OH terminus of the tRNA on the tRNA-adenylate and the two termini are joined via a phosphodiester bond, the AMP is released. | Rnl1 is in fact a tRNA repair enzyme used by the T4 bacteriophage to escape hosts antiviral response. Enzyme functioning requires ATP and divalent metal ions. The T4 ligase repairs the tRNA<sup>Lys</sup> by joining its 5'-PO<sub>4</sub> and 3'-OH groups via series of three nucleotidyl transfer steps in a ping-pong enzymatic mechanism. First, the Lys<sup>99</sup> of the enzyme reacts with the a phosphorus of ATP and forms a covalent intermediate: ligase-(lysyl-N)-AMP. Pyrophosphate is also produced during this step. Secondly, AMP is transferred from the intermediate to the 5'- PO<sub>4</sub> terminus of a tRNA to form an tRNA-adenylate intermediate (AppRNA). Finally, the ligase catalyzes the attack of the 3'-OH terminus of the tRNA on the tRNA-adenylate and the two termini are joined via a phosphodiester bond, the AMP is released. | ||
<br/><br/> | <br/><br/><br/> | ||
==Biological role== | ==Biological role== | ||
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::* In the second step, AMP is transferred from the covalent intermediate to the 5'-phosphate RNA, forming a tRNA-adenylate intermediate (AppRNA). Arg54, by stabilizing and orienting the RNA phosphate by hydrogen bonding, is essential for this RNA adenylation.<ref name="main_article" /> | ::* In the second step, AMP is transferred from the covalent intermediate to the 5'-phosphate RNA, forming a tRNA-adenylate intermediate (AppRNA). Arg54, by stabilizing and orienting the RNA phosphate by hydrogen bonding, is essential for this RNA adenylation.<ref name="main_article" /> | ||
::* In the third step, the 3'-hydroxyl RNA attacks the 5'-phosphate RNA. A phosphodiester bond is formed and an AMP is released. | ::* In the third step, the 3'-hydroxyl RNA attacks the 5'-phosphate RNA. A phosphodiester bond is formed and an AMP is released. | ||
==See Also== | |||
*[[T4 RNA ligase 2 (Rnl2)]] | |||
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*[http://www.ebi.ac.uk/pdbsum/2c5u PDBsum file on 2C5U] | *[http://www.ebi.ac.uk/pdbsum/2c5u PDBsum file on 2C5U] | ||
*[http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c5u OCA Atlas for 2C5U] | *[http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c5u OCA Atlas for 2C5U] | ||
==References== | ==References== | ||
<references /> | <references /> | ||
