The Hexameric Helicase DnaB Adopts a Nonplanar Conformation during Translocation

SummaryDNA polymerases can only synthesize nascent DNA from single-stranded DNA (ssDNA) templates. In bacteria, the unwinding of parental duplex DNA is carried out by the replicative DNA helicase (DnaB) that couples NTP hydrolysis to 5′ to 3′ translocation. The crystal structure of the DnaB hexamer in complex with GDP-AlF4 and ssDNA reported here reveals that DnaB adopts a closed spiral staircase quaternary structure around an A-form ssDNA with each C-terminal domain coordinating two nucleotides of ssDNA. The structure not only provides structural insights into the translocation mechanism of superfamily IV helicases but also suggests that members of this superfamily employ a translocation mechanism that is distinct from other helicase superfamilies. We propose a hand-over-hand mechanism in which sequential hydrolysis of NTP causes a sequential 5′ to 3′ movement of the subunits along the helical axis of the staircase, resulting in the unwinding of two nucleotides per subunit.

Graphical AbstractFigure optionsDownload high-quality image (466 K)Download as PowerPoint slideHighlights
► Hexameric helicase DnaB forms a spiral staircase in complex with ssDNA and GDP-AlF4
► DnaB binds to an A-form ssDNA with a step size of two nucleotides per subunit
► Translocation can be modeled as moving each subunit in a hand-over-hand mechanism
► Subunit movement along DNA is mechanistically distinct from other hexameric helicases