Figure 10

Schematic model for the IS 2 transposition pathway. Each synaptic complex is shown as a dimer with a DNA binding site (BS; orange) to which protein binding domains (PBD) of the right and left inverted repeats (IRR, red and IRL, green) are bound, and a catalytic center (CC; pink). Each CC possesses a binding tract (orientation I), for the extensive sequence-specific binding of the cleavage domain (CD) and a tract (yellow band; orientation II), at which target or host DNA may be complexed selectively and/or non-specifically. (A) Synaptic Complex I. The CD of IRR is bound in orientation I in cis at its cognate active CC. The IRL CD is bent (asterisk) and complexed at the active CC in trans in orientation II, with adjacent host DNA (bold black lines). The 3'OH tip of the cleaved IRR CD is positioned at a 3' 5' phosphodiester bond between the first and second residues of the host DNA near the 5' end of the tip of IRL. Broken black lines represent the coding sequence of IS2. (B) Synaptic Complex II- first phase. Abutted CDs of the MCJ separated by a single base pair spacer (bold black dot), are bound in orientation I at the active IRR CC. Trans binding of the IRL CD is facilitated by two bends (asterisks), within the CD and at the outer end of the PBD. Red arrows identify sequential single-strand cleavages at the 3' ends of the CDs. (C) Synaptic Complex II- second phase. The CD of IRL, free from flanking DNA, binds to its cognate CC in orientation I. Exposed 3'OH groups at the ends of both CDs (half arrows) are juxtaposed to the target DNA, non-specifically bound (curved bold black lines) in the orientation II tracts of the CCs. BS: binding site; CC: catalytic center; CD: cleavage domain; IRR/IRL: right and left inverted repeats; MCJ: minicircle junction; PBD: protein binding domain.