at its narrowest point of 36 Å, which is large enough to accommodate the duplex DNA. The negative charge
of the ring might electrostatically impede the exit of the compacted DNA. A second ring is composed of
five subunits, and is therefore a symmetry mismatch with the 12-membered ring. The subunits are RNA–
protein complexes that undergo conformational change upon binding and hydrolysis of ATP, and it is pos-
sible that this conformational switch may lead to asymmetry around the ring, just as in the case of the T7
helicase and F1 ATPase mentioned above (Figure 10.20b). The dodecameric connector may rotate in
response to ATP binding and hydrolysis. To preserve its interaction with the connector, the DNA must trans-
late along its helical axis by 1/5th its pitch, corresponding to two base pair steps for B-form DNA (Figure
10.20b). Thus, the pump is cleverly designed to convert the mismatch of molecular symmetries between
the two rings and the DNA into a translational displacement of the DNA.
An analogous pumping mechanism may occur in the export of DNA by bacteria during transfer of plas-
mid DNA (‘conjugation’) viaa hexameric ATPase. Here, the DNA must move across a lipid-bilayer mem-
brane, which is a very strong permeability barrier to the nucleic acid. The pump acts as an energy-inducible,
selective channel that transports the DNA vectorially.52,53The protomer of the hexameric pump has struc-
tural similarity with the RecA ATPase that forms helical filaments on single-stranded DNA.^54 It seems likely
that, during the translocation process, each protomer may interact with the DNA in a similar fashion to
Protein–Nucleic Acid Interactions 415
Figure 10.20 (a) The crystal structure of the central component of the motor from Bacillus subtilis bacteriophage
f29 illustrates the principle of operation of DNA pumps (PDB: 1H5W). The panel on the left is a view
down the molecular 12-fold axis and on the right is the side view. (b) A schematic of the
mismatched symmetries of the five helicase subunits, the 12 portal proteins, and the duplex DNA. The
asterisk indicates the point of contact of the DNA with the portal protein, which changes during rota-
tion of the portal ring
(Figure kindly provided by F. Anson, University of York)