Fig. 4: Structural mechanism of N34 recognition by the C-ter C domain of eukaryotic/archaeal-type IleRS.
a The binding of G34 to the C-ter C domain of ScIleRS. The top panel shows a zoomed-in view of the G34 binding site of the ScIleRS·tRNAIle(GAU)·l-Ile complex. Direct and water-mediated H-bonding interactions are shown as black dashed lines. The bottom panel is the 2D presentation of G34–residues interactions, and the direct H-bonds are shown as orange dashed lines. The water-mediated H-bonding interactions have been omitted in the 2D presentation. b 2D presentations of the modeling of A34 and I34 at the N34 binding site of ScIleRS. A34 is unable to interact with the N34 binding residues due to the lack of appropriate H-bond acceptors or donors, so it is poorly recognized by ScIleRS. In contrast, after deamination, I34 can bind to these residues like G34, and be well recognized by ScIleRS. c Modeling of U34 and Ψ34 at the N34 binding site of ScIleRS. d Modeling of C34 and agm2C34 at the N34 binding sites of ScIleRS and PhIleRS, respectively.
