The antibiotic bicyclomycin inhibits rho-dependent termination processes by
interfering with RNA translocation by preventing RNA binding at the transl
ocation site or by uncoupling the translocation process from ATP hydrolysis
. Previous studies have shown that bicyclomycin binds near the ATP hydrolys
is pocket on rho. The hexameric structure of rho indicates that it is in a
class of enzymes with strong sequence similarity to F-1-ATP synthase. The b
icyclomycin derivative 5a-formylbicyclomycin, an inhibitor comparable to bi
cyclomycin, was previously shown to form a stable imine with rho and when r
educed to the amine with NaBH4 to singly label five of the six rho subunits
. Lysine-336 was identified by mass spectrometric analysis of trypsin-diges
ted fragments as the site of 5a-formylbicyclomycin adduction. A model of rh
o was made by threading the rho sequence on the known crystal structure of
the alpha and beta subunits of F-1-ATP synthase. The model, along with info
rmation concerning the extent and site of 5a-formylbicyclomycin adduction,
indicates an overall C6 symmetry for rho subunit organization. We propose t
hat the sequence similarity between rho and F-1-ATP synthase extends to a s
imilar quaternary structure and an equivalent enzyme mechanism. The propose
d mechanism of RNA translocation coupled with ATP hydrolysis changes the ov
erall symmetry of rho from C6 to C6/C3.