A DNA translocase operates by cycling between planar and lock-washer structures

Abstract

Ring ATPases that translocate disordered polymers possess lock-washer architectures that they impose on their substrates during transport via a hand-over-hand mechanism. Here, we investigate the operation of ring motors that transport substrates possessing a preexisting helical structure, such as the bacteriophage ϕ29 dsDNA packaging motor. During each cycle, this pentameric motor tracks one helix strand (the ‘tracking strand’), and alternates between two segregated phases: a dwell in which it exchanges ADP for ATP and a burst in which it packages a full turn of DNA in four steps. We challenge this motor with DNA-RNA hybrids and dsRNA substrates and find that it adapts the size of its burst to the corresponding shorter helical pitches by keeping three of its power strokes invariant while shortening the fourth. Intermittently, the motor loses grip when the tracking strand is RNA, indicating that it makes load-bearing contacts with the substrate that are optimal with dsDNA. The motor possesses weaker grip when ADP-bound at the end of the burst. To rationalize all these observations, we propose a helical inchworm translocation mechanism in which the motor increasingly adopts a lock-washer structure during the ATP loading dwell and successively regains its planar form with each power stroke during the burst.