Predicted secondary structures of RNase P RNAs (P RNAs) from (A) T. indicus, (B) M. infernorum, and (C) T. maritima in a secondary structure presentation attuned to (D) the 3D structure of the T. maritima P RNA as part of the RNase P holoenzyme (Massire et al. 1998; Reiter et al. 2010). (A–C) Coaxially stacked helices are of the same color and the five regions with highest sequence conservation (CR-I to CR-V), which cluster in two regions, are highlighted; CR-I and CR-V overlap with helix P4. The gray broken line separates the catalytic (C-) and specificity (S-) domains. Tertiary contacts (according to the T. maritima RNase P holoenzyme structure; Reiter et al. 2010) are marked by thin dotted lines connecting boxed or circled elements; question marks were added to indicate that formation of this contact in the respective RNA is unclear due to structural variation. Sequences that lack P19 possess instead a 4 nt linker (R19) (Massire et al. 1998). Noncanonical structure elements in panel B (P16.1, P18.1) are drawn in gray. The 5′-GGU motif in loop 15 (L15) interacting with the CCA end of tRNA molecules is highlighted in panel B. (D) Adapted with permission from Gößringer et al. (2021). Structural elements are colored as in panel A–C. Ochre spheres represent two active site metal ions (Me1/2) and two structurally important metal ions (Me3, Me4; Reiter et al. 2010).
