FIG. 15.

Model for RecBCD enzyme mechanism (see the text for details). (A) Cartoon representation of the initiation complex as seen in Fig. 8. The three subunits are color coded as described above, with important functional regions in the structure also labeled. (B) Pre-Chi recognition. RecBCD travels along duplex DNA powered by ATP hydrolysis in the RecB and RecD helicase motors. RecD can be the faster motor, and consequently, a loop of ssDNA may form ahead of the slower RecB motor. The RecB nuclease domain is most favorably positioned to cleave the 3′ ssDNA tail, and this strand is therefore hydrolyzed much more vigorously than the 5′ ssDNA tail. Between the RecB motor and the nuclease domain, the 3′ ssDNA tail is scanned for the Chi sequence as it passes through a tunnel in the RecC protein. (C) The Chi sequence is recognized and remains tightly bound in a tunnel in the RecC protein. The complex pauses before translocation resumes at a reduced rate. Exit of the 3′ ssDNA tail is prevented, and so a final cleavage event takes place on this strand just upstream of the Chi sequence. The 5′ ssDNA strand continues to exit from the rear of the enzyme, where, in the absence of competition from the complementary strand, it is now cleaved more readily by the nuclease domain. A loop of ssDNA accumulates downstream of the Chi sequence. The RecB nuclease domain undocks, recruits RecA proteins from solution, and loads them onto the growing ssDNA loop to promote RecA nucleoprotein filament formation. This process is proposed to be triggered by the release of the RecB nuclease domain from RecC following Chi recognition.