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

Models of bisubstrate complexes of PhoTpt1 bound to NAD⁺ and either 2′-PO₄ RNA or 5′-AMP. (A) A Tpt1 bisubstrate complex with the junction nucleotide pA^2′Pp and NAD⁺ was modeled by superimposing the Tpt1•ApA^2′PpA and Tpt1•NAD⁺ structures. Hydrogen bonds to the 2′-PO₄, the NAD⁺ phosphates, and the NAD⁺ nicotinamide are denoted by black dashed lines. The distance from the 2′-PO₄ to the C1″ atom of NAD⁺ is indicated by a green dashed line. (B) A bisubstrate complex with 5′-AMP and NAD⁺ was modeled by superimposing the Tpt1•5′-AMP and Tpt1•NAD⁺ structures. Hydrogen bonds to the 5′-PO₄ are denoted by black dashed lines. The distance from the 5′-PO₄ to the C1″ atom of NAD⁺ is indicated by a green dashed line.