Figure 4.

Structural comparison of Abi proteins with group II intron maturase and HIV-1 reverse transcriptase. Structures of G. stearothermophilus maturase (PDB ID: 6AR1(38)) (A), Ll-AbiK (B), Abi-P2 (C) and HIV-1 RT (PDB ID: 4PQU(40)) (D) are shown in two orientations. Domains are color-coded: palm, red; fingers, blue; helical domain, yellow; thumb, green; connection domain, teal; RNase H, orange; DNA-binding domain, violet. The p51 subunit of HIV-1 RT is shown in gray. DNA and RNA strands in substrates are shown as cartoon and colored blue and red, respectively. (E) Sequence alignment of fingers/palm portion of Ll-AbiK and Abi-P2 polymerases with corresponding regions of L. lactis AbiA, G. stearothermophilus maturase and HIV-1 RT (output from PROMALS3D (41)). The alignment was truncated to show only the regions that can be reliably superimposed structurally. Residue ranges corresponding to fingers and palm domains are marked below the alignment with green and yellow lines, respectively. Secondary structure elements are indicated with colors – α-helices in red, β-strands in blue. Active site residues are highlighted in green. Positions at which substitutions were introduced in Ll-AbiK are indicated with asterisks above the alignment.