Figure 10

Structure-based alignments of middle interval and catalytic active site elements of IS 3 -family transposases and HIV-1 and Rous sarcoma virus integrases. (A) α helices identified in the middle interval of the IS2 transposase (TPase) and the corresponding sequences of five other members of the principal sub-groups in the IS3 family. Where applicable, the sequences of corresponding elements in the Rous sarcoma virus (RSV) and the HIV-1 were also aligned (red lettering). All coordinates are those of IS2. Functionally conserved non-polar hydrophobic residues are highlighted in yellow and identified as h1 and h2 (Methods - alignment tools). Functionally conserved basic residues (b) are highlighted in blue. NA = no alignments identified in the integrases of RSV and HIV-1. (B) α helices and β strands in the catalytic active sites (CASs) of the TPases of IS2, five other IS3 family members, and the integrases of RSV and HIV-1 (red lettering). Functionally conserved hydrophobic and basic residues are identified as described in part A. In addition, functionally conserved acidic residues or their amides (a) are highlighted in purple, non-polar aromatics (aro) in green, polar serines and/or threonines (p) in orange and prolines (pro) in mauve. DDE residues are indicated by large black dots. Sequences in parentheses are not components of the α helices or β strands. α helix 2 (2+3) in the TPases aligns with helices 2 and 3 in the integrases. Residues conserved in α helix 2 of the integrases and in its remnants in IS407, are enclosed in a black rectangle. Large double asterisks indicate short α helices with no homology to other sequences (see part C graphic). Substitutions are indicated by red ovals; twin ovals indicate A341P and A341T. (C) Graphic alignment of α helices and β strands of the CASs of the TPases of IS2 and five other members of the IS3 family and of the integrases of RSV and HIV-1. Black dots within the elements represent the positions of the DDE triad. DDE: the catalytic triad of two aspartates and a glutamate; CAS: catalytic active site; IS: insertion sequence; RSV: Rous sarcoma virus; TPase: transposase.