Extended Data Fig. 10: Structural model for the interaction between Arabidopsis PRORP2, a pre-tRNA and TRM1A.
From: A tRNA-modifying enzyme facilitates RNase P activity in Arabidopsis nuclei
a PRORP2 experimental crystal structure is shown in brown shades, a representative pre-tRNA is shown in purple with the position of G26 highlighted. PRORP2 binding to tRNA is represented according to experimental biochemical and biophysical results9 and PRORP2 pre-tRNA cleavage site is shown by a red star. Arabidopsis TRM1A structure model was built with AlphaFold 2.050 and its docking to tRNA is represented according to the experimental biochemical analysis of Aquifex aeolicus TRM1 binding to tRNA40. TRM1A C-terminal domain is shown in pink, whereas its N-terminal catalytic domain is shown in light blue. TRM1 catalytic pocket is represented in yellow. b TRM1A model generated by AlphaFold is colored according to model confidence, that is with dark blue part of the protein including the catalytic domain and the protein regions shown to interact with tRNA in Aquifex aeolicus40 having very high model confidence. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions below 50 pLDDT may be unstructured.
