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 ordered, helical substrates, such as the bacteriophage ϕ29 dsDNA packaging motor. This pentameric motor alternates between an ATP loading dwell and a hydrolysis burst wherein it packages one turn of DNA in four steps. When challenged with DNA-RNA hybrids and dsRNA, the motor matches its burst to the shorter helical pitches, keeping three power strokes invariant while shortening the fourth. Intermittently, the motor loses grip on the RNA-containing substrates, indicating that it makes optimal load-bearing contacts with dsDNA. To rationalize these observations, we propose a helical inchworm translocation mechanism in which, during each cycle, 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.
Highlights
Ring ATPases that translocate disordered polymers possess lock-washer architectures that they impose on their substrates during transport via a hand-over-hand mechanism
We investigate how the structure and symmetry properties of the substrate determine the stepping mechanism of the DNA-packaging motor of bacteriophage φ29, which has recently been shown to adopt a lock-washer structure in which the individual subunits contact the phosphates of the DNA backbone[13]
Each burst is made of four 2.5 bp steps (0.85 nm), indicating that one of the five subunits is special in that it does not perform a mechanical but a regulatory function[5,7]. This task requires the special subunit to contact a pair of phosphates in the strand that is being packaged in the 5′ to 3′ direction every pitch[4]. All of these properties are incompatible with the hand-over-hand mechanism proposed in the literature, where nucleotide exchange and hydrolysis are interlaced, every subunit is functionally identical, and translocation occurs in pairs of substrate monomers[10,11,12]
Summary
Ring ATPases that translocate disordered polymers possess lock-washer architectures that they impose on their substrates during transport via a hand-over-hand mechanism. We propose a model for the packaging mechanism in which the ring cracks open, progressively adopting a lock-washer conformation during the ATP loading dwell, and successively returns to a planar structure upon sequential hydrolysis during the translocation burst.
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