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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.


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==Biological role==
==Biological role==


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</StructureSection>
</StructureSection>
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==Chemical reaction==




==Chemical reaction==
:The T4 RNA ligase (Enzyme class : E.C.6.5.1.3) catalyzes the formation of phosphodiester bonds between the 5'-phosphate terminus of single-stranded nucleic acid (i) and the 3'-hydroxyl terminus of single-stranded nucleic acid (j).
 
 
:'''ATP + ribonucleotide<sub>(i)</sub> + ribonucleotide<sub>(j)</sub> → AMP + diphosphate + ribonucleotide<sub>(i+j)</sub>'''
 
 
:Rnl1 catalysis involves three steps :
::* In the first step, Lys99 in the conserved motif KX(D/N)G (motif I) reacts with the α-phosphate of ATP or ATP analogue (NAD or GTP) and forms a covalent bond. This step gives a covalent intermediate ligase-(lysyl-N)-AMP and a pyrophosphate. Lys99, which is responsible for this step, is the essential residue involved in the catalytic mechanism.<ref>Shuman, S., and Schwer, B. (1995) Mol. Microbiol. 17, 405–410</ref>
::* 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.
 


The T4 RNA ligase (Enzyme class : E.C.6.5.1.3) catalyzes the formation of phosphodiester bonds between the 5'-phosphate terminus of single-stranded nucleic acid (i) and the 3'-hydroxyl terminus of single-stranded nucleic acid (j).


ATP + ribonucleotide<sub>(i)</sub> + ribonucleotide<sub>(j)</sub> → AMP + diphosphate + ribonucleotide<sub>(i+j)</sub>
==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 />
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