Mechanisms by which G-patch activators tune the processive multi-tasking ATP-dependent RNA helicase Prp43 to remodel diverse RNA:protein complexes remain elusive. Here, a comparative study between a new activator, Tma23, and a characterized activator, Pxr1, uncovered segments that organize Prp43 function during ribosome assembly. In addition to the activating G-patch, we discovered an inhibitory segment within Tma23 and Pxr1, I-patch, that restrains Prp43-ATPase activity. Cryo-electron microscopy and hydrogen-deuterium exchange mass spectrometry show how I-patch binds to the catalytic RecA-like domains to allosterically inhibit Prp43-ATPase activity. Tma23 and Pxr1 also contain a dimerization segment which organizes Prp43 into higher-order complexes. We posit that Prp43 function at discrete locations on pre-ribosomal RNA are coordinated through toggling interactions with G-patch and I-patch motifs. This could guarantee measured and timely Prp43 activation, enabling precise control over multiple RNA remodeling events occurring concurrently during ribosome formation.