Fig. 5

A Comparison of domain architechture of R2Bm, Prp8, and LtrA group II intron proteins. a The amino acid equivalences between ΔNR2Bm and that of the full length R2Bm ORF (genbank entry M16558.1) is such that the 2nd amino acid of the ΔNR2Bm ORF is 70th amino acid of full length R2Bm. b The ORF structure of ΔNR2Bm, S. cerevisiae Prp8, and L. lactis LtrA are presented as a colored bar diagrams. The RT is green, the linker is a maroon, and the RLE is orange. The RT sequence-motif blocks are indicated with approximate primary amino acid numbers. The locations of the fingers are also shown. The bar diagrams are not drawn to scale. The domains and numbering for Prp8 and LtrA group II intron are largely from [22, 52, 70, 71]. Brackets indicate regions of R2Bm that align well with corresponding region of Prp8. The RT and the RLE align well in sequence and by structure modeling with Prp8. In the linker, the sequence of (and around) the colored α-helices (rounded bars) with an asterisk align when well when anchored by the reverse transcriptase and the RLE. The colored β-strands and the α-helix lacking an asterisk do not align well but (may) form a knuckle that is structurally similar. The secondary structure is predicted in R2Bm, but known in Prp8 (3JCM). c Ribbon diagrams of the R2Bm RT and RLE models. The ribbons have been colored as in the the cooresponding bar diagram. d Ribbon diagrams of the Prp8 cryo-EM structure (3JCM, RT to RLE) is shown in matching color bar diagram. e Ribbon overlay of R2Bm (tan) with Prp8 large fragment (blue). f The R2Bm reverse transcriptase model as colored in Fig. 3e, a ribbon model of the R2Bm RLE and the large fragment of Prp8 (blue with red 1585 loop and knuckle). Abbreviations: palm traversing helix (pth); DNA binding domain (DBD); Endonuclease (EN). All other abbreviations and symbols are as in previous figures