Schematics depicting alternative configurations of the N-domain and
arm-type site interactions in the integrative and excisive Holliday junction
recombination intermediates. The symbols and notation are the same as in
Fig. 1,
B–D, protein-bound sites are denoted by
white symbols, unbound sites are in gray symbols, and
solid heavy arrows denote where arm DNA is joined to the branches of
the HJ. In the excisive HJ intermediate, three arm-type sites (P2, P′1,
and P′2) are bound by the indicated N-domains, with a fourth N-domain
either interacting with Xis (A) or free in solution (B). In
the integrative HJ complex, four arm-type sites(P1, P′1, P′2, and
P′3) are bound by N-domains of the Int tetramer. Accommodation of the
third P′ arm-type site is achieved either by primarily altering the
trajectory of the P′ arm DNA (C), by altering the orientation
and position of the N-domain/linker region (D), or by some
combination of both (see “discussion” and
Fig. 1B).