Sandbox 201: Difference between revisions
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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). | :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> | * ATP + ribonucleotide<sub>(i)</sub> + ribonucleotide<sub>(j)</sub> → AMP + diphosphate + ribonucleotide<sub>(i+j)</sub> | ||
:The essential residue involved in the catalytic mechanism is Lys99 in the conserved motif KX(D/N)G (motif I). | |||
:Rnl1 catalysis involves three steps : | |||
::In the first step, Lys 99 reacts with the alpha�-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. | |||
::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. | |||
