tRNA charging.txt

aka aminoacylation of tRNA: the process by which the correct amino acid is attached to its cognate tRNA.

aminoacyl-tRNA synthase (RS)

• 1. A single RS is used for each for each amino acid..recognizing different nucleotides of the 4 arms and variable loop of tRNA, aka '2nd operational genetic code'
• 2. ATP is needed to provide energy for the reaction
• 3. aa (amino acid) gets attached to the acceptor arm by a specific RS
• 4. Aminoacyl-AMP (Aa-AMP) intermediate is formed during the charging process.

• tRNA is a small molecule (~80 Nt residues) that is t-shaped
• w/ 4 arms ( D arm, anticodon arm, TΨC arm, & acceptor arm)
• w/ variable loop

• RS can recognize the active site pocket (how aa fits into ligand pocket)
• Class I, aa interacts with KMSK and HIGH motifs
• RS makes sure aa is able to form bonds to metal cations
• RS can remove BAD AA after charging

• Class I: aa-AMP first attaches to C-2 (carbon of OH ribose sugar) & transferred via transesterification to C-3
• It is specific for 10 aa
• mainly a MONOMER
• active site SHORT (170 aa)
• active site on LEFT side of RS
• RS approaches tRNA acceptor end from MINOR groove
• Uses Zn binding domain
• Contains Rossman fold motif & uses KMSK & HIGH motifs in active site for charging aa

• aa-AMP attached to C-3 (3rd carbon OH-ribose sugar)
• specific for 10 aa
• mainly a DIMER
• active site LARGE (250aa)
• active site located on RIGHT side of RS
• RS approaches tRNA acceptor end from MAJOR groove
• Contains motifs 1, 2 & 3

• Type 1: before Aa-charging editing (pre-transfer editing)
• 1. Aa-AMP intermediate is formed
• 2. Aa-AMP is checked if it fits in the editing site
• 3. if Aa-AMP DOES NOT fit, it is kept(correct Aa)

• ..it is removed (bad AA)
• 1. Correct Aa-AMP is attached to tRNA, (eventually the AMP is removed

• 1. Aa-AMP intermediate is formed
• 2. Bad Aa-AMP is attached to tRNA (eventually the AMP is removed
• 3. Bad Aa-tRNA is checked into editing site
• Bad Aa is removed (bad AA)