We have solved two structures of PcrA helicase in complex with a true DNA substrate. In the first structure PcrA is bound to a partial duplex DNA (10 base pairs and a 7 base 3' single stranded overhang) and to ADPNP (a non-hydrolysable analogue of ATP). This structure represents a snapshot of the helicase before ATP hydrolysis and we therefore refer to it as the "substrate complex". The second structure consists of PcrA bound to the same DNA substrate and a sulphate ion. The sulphate ion occupies the position of the phosphate ion after ATP hydrolysis and so we refer to this as a "product complex".

Macromolecular motions
Comparison of the apo, substrate and product complexes reveals large conformational changes associated with DNA binding and with nucleotide binding and hydrolysis. Using the excellent morph server available here, we have been able to create movies which help to show the nature of these movements clearly.

Model for single stranded DNA translocation

On the basis of the substrate and product complexes of PcrA we have proposed a model for how the free energy of ATP hydrolysis is harnessed to create a single stranded DNA tracking motor.

Modified inchworm model for PcrA catalysed helicase activity
We propose a model in which PcrA catalysed helicase activity comprises two structurally distinct but coupled activities. Firstly, the protein contains a single stranded DNA motor (above), hydrolysing one ATP per base translocated. Secondly the protein undergoes ATP dependent conformational changes which actively distort the duplex DNA ahead of the progressing ssDNA tracking motor, presumably aiding in its progress.