Structures of RNA phosphotransferase Tpt1 reveal distinct binding modes for an RNA 2′-PO₄ splice junction versus a 5′-PO₄ mononucleotide

Surface electrostatics and atomic interaction with 2′-PO₄ RNA. (A) Surface electrostatic model of the binary substrate complex of PhoTpt1 with ApA^2′PpA. The junction adenosine nucleobase is flipped into a deep crevice in the RNA lobe. (B) Stereo view highlighting atomic interactions of the junction nucleotide pA^2′Pp (stick model with gray carbons) with Tpt1 amino acids (stick models with beige carbons). Hydrogen bonds are denoted by black dashed lines. Van der Waals contacts are depicted as beige dashed lines.