 | Acta Crystallographica Section D Acta Crystallographica Section D BIOLOGICAL CRYSTALLOGRAPHY |
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![[Figure 5]](be5126fig5mag.jpg)
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Figure 5
Hypothetical model of ATP hydrolysis-facilitated gap displacement. The crystallized protein filament is shown as a Cα trace in salmon with AMPPNP in green. Speculative models of the DNA substrates are shown as wires. Important segments are boxed. The 5′- and 3′-ends are based on the filament-initiating ssDNA (thinner wire in blue). The homologous dsDNA is shown as a thicker wire in yellow. The strand-exchange process progresses from the 5′-end to the 3′-end. (a) An intervening gap. Such gaps are likely to exist owing to simultaneous homologous pairing between the recombinase/ssDNA filament and dsDNA at multiple locations. The dsDNA in the gap region cannot become properly wound (∼19 bp per helical turn) around the nucleoprotein filament without unwinding its adjacent region(s). Despite the sequence homology, it serves as a topological roadblock of strand exchange between long DNA substrates. (b) ATP hydrolysis promotes the transient release of a dsDNA segment at the immediate 3′-flank of the gap. The transiently released dsDNA region is shown as an exaggerated wide helix. (c) Rearrangement in the transiently released dsDNA region and the adjacent gap takes place without changing the overall topology. The 5′-end of the gap region becomes properly wound, while the released dsDNA region becomes unwound. (d) The rearranged 5′-end of the gap becomes bound by the recombinase filament. As a result, the gap is displaced towards the 3′-end. (e) Repetition of steps (b)–(d) would chase the topologically strained gap out of the 3′-end of the nucleoprotein filament, therefore removing topological roadblocks to extensive DNA strand exchange. |
![[Figure 5]](be5126fig5.jpg)
| BIOLOGICAL CRYSTALLOGRAPHY |
ISSN: 1399-0047
