Supplementary Figure 6: Structure-based sequence alignment of the RT and EN domains.

Structure based sequence alignments are performed using PROMALS3D ⁴⁵. (a) Structure based sequence alignment of the RT fingers-palm domains of LtrA and Tribolium castaneum TERT (PDB: 3DU5). Secondary structures are shown with arrows for β-strands and bars for α helices. Identical residues are shaded in grey and indicated underneath with asterisks. Residues involved in TPRT in TERT and corresponding residues in LtrA are highlighted in different colors. Red, catalytic residues; Turquoise, dNTP binding pocket; Green, DNA primer grip; Purple, RNA template interaction. (b) Alignment of the RT thumb domains of LtrA and Saccharomyces cerevisiae Prp8 (PDB: 3ZEF). α-helices are shown as bars, identical residues are shaded in grey and indicated underneath with asterisks. (c) Structure based sequence alignment of the EN domains from LtrA and the putative HNH endonuclease Gmet_0936 protein from Geobacter metallireducens GS-15 (PDB: 4H9D), HNH homing endonuclease I-HmuI (PDB: 1U3E), and E7 toxin (PDB: 1MZ8). Secondary structures are shown with arrows for β-strands and bars for α helices. The typical HNH motif residues are in red and four cysteine residues conserved between LtrA and Geobacter HNH endonuclease and proposed to be in additional metal ion coordination are in magenta. (d) Structure based sequence alignment of RT fingers-palm and thumb domains from LtrA, TERT, Prp8, and HIV-1 RT (PDB: 2HMI). Conserved sequence blocks RT1-RT7 in the fingers- palm domains (rectangular boxes) and the three parallel helices from Prp8 (H1-H3, boxes are in red, orange and green, as in panel b) in thumb domains in LtrA, TERT and HIV-1 RT, are defined using HIV-1 RT and Prp8 as references, respectively. Sequences in α-helices and β-strands are in red and blue, respectively. Insertions between RT sequence blocks, 2a, 4a, 5a, and 7a, and the thumb insertion ti are shown and labeled in red. Sequences of IFD-like motifs, are shaded in grey. Conserved aspartic acid residues at the RT active site are marked by red arrows. Motifs 1, 2, A, B’, C, D, E (tan letters) in Tribolium castaneum TERT are in dark red boxes. Sequences that are not structurally resolved are boxed with dashed grey lines.