Schematic depiction of an effective RNA substrate of AvaPnkp/Hen1 and its repaired product based on experimental data presented in this study. The two terminal nucleotides to be ligated by AvaPnkp/Hen1 are highlighted in gray, with the depicted 5′-OH and 2′,3′-cyclic phosphate groups that are directly involved in repair chemistry. ATP is required for phosphorylation of the 5′-OH group, and AdoMet is the methyl donor for 2′-O-methylation on the 3′-terminal nucleotide during repair, which requires a manganese ion (Mn2+) to carry out the reaction. The numbers of nucleotides for the different regions of RNA (5′ overhang, 3′ overhang, Stem 1, Bulge, and Stem 2) were chosen arbitrarily. Secondary structures of the Bulge, the 5′ overhang, the 3′ overhang, and the resulting repaired loop were also arbitrary depicted.
