Running in Reverse: The Structural Basis for Translocation Polarity in Hexameric Helicases

Abstract

Summary Hexameric helicases couple ATP hydrolysis to processive separation of nucleic acid duplexes, a process critical for gene expression, DNA replication and repair. All hexameric helicases fall into two families with opposing translocation polarities: the 3’→5’ AAA+ and 5’→3’ RecA-like enzymes. To understand how a RecA-like hexameric helicase engages and translocates along substrate, we determined the structure of the E. coli Rho transcription termination factor bound to RNA and nucleotide. Interior nucleic-acid binding elements spiral around six bases of RNA in a manner unexpectedly reminiscent of an AAA+ helicase, the papillomavirus E1 protein. Four distinct ATP-binding states, representing potential catalytic intermediates, are coupled to RNA positioning through a complex allosteric network. Comparative studies with E1 suggest that RecA and AAA+ hexameric helicases use different portions of their chemomechanical cycle for translocating nucleic acid, and track in opposite directions by reversing the firing order of ATPase sites around the hexameric ring.