COMPLEX OF ESCHERICHIA-COLI PRIMARY REPLICATIVE HELICASE DNAB PROTEINWITH A REPLICATION FORK - RECOGNITION AND STRUCTURE

Interactions of the Escherichia coli replicative helicase DnaB protein , with DNA replication fork substrates, have been studied using rigoro us fluorescence titration, fluorescence energy transfer, and analytica l ultracentrifugation methods. DnaB binds the 5' single-arm fork, the 3' single-arm fork, and the two-arm fork with stoichiometries of 1, 1, and 2 DnaB hexamers per fork, independent of the length of the duplex part of the fork. Within the structurally heterogeneous binding site, the helicase accesses most of the 20 nucleotide residues of an arm. T he dsDNA of the fork does not contribute to the affinity; however, it affects the positioning of the enzyme on the 5' or 3' arm. Fluorescenc e energy transfer experiments provide direct evidence that the DnaB he licase binds the 5' arm of the fork in a single orientation, with resp ect to the duplex part of the fork. The 33-kDa domains of the hexamer face the dsDNA, while the small 12-kDa domains face the 5' end of the arm. In the complex with the 3' arm, the helicase is bound in an oppos ite orientation when compared to the 5' arm. This is the first determi nation of the strict, single orientation of a helicase in the complex with a replication fork. The 3' arm accommodates a DnaB hexamer, while another hexamer is associated with the 5' arm. The complex of two Dna B hexamers bound in opposite orientations with each arm of the fork ma y play an important role during bidirectional replication of the E. co li DNA.