Non-hexameric DNA helicases and translocases: mechanisms and regulation

Abstract

The superfamily 1 (SF1) and SF2 enzymes are non-hexameric enzymes possessing both helicase and single-stranded DNA (ssDNA) translocase activities, as well as the ability to displace proteins from DNA. In general, the same oligomeric form of these enzymes is not responsible for all of these activities. For some SF1 enzymes, ssDNA-translocase activity is not sufficient for helicase activity, hence these two activities are separable. The monomeric form of some SF1 enzymes are rapid and processive ssDNA translocases, but have subdomains that are autoinhibitory for monomer helicase activity; activation of helicase activity requires self-assembly (oligomerization) or interactions with accessory proteins. This might serve to regulate the enzyme so that it can function as a translocase to displace proteins from the DNA under conditions such that its helicase activity is suppressed. During ssDNA translocation of PcrA and UvrD monomers, the hydrolysis of one molecule of ATP is coupled to movement by one base along the DNA. However, in many cases, larger translocation steps of variable size have been observed from single molecule measurements or calculated from pre-steady-state ensemble kinetic studies suggesting non-uniform translocation mechanisms. Current evidence suggests that many helicases unwind DNA by facilitating the destabilization of the double-stranded DNA (an active mechanism), rather than by translocating into a single-stranded DNA region formed through thermal fluctuations (so-called 'breathing') of the duplex at a ssDNA–dsDNA junction. High resolution crystal structures of SF1 enzymes in complex with DNA and various nucleotide analogues have led to detailed proposals for ssDNA translocation through 'inch-worm' mechanisms that involve relative movements of two subdomains, the interface of which forms the ATP-binding site. Whether the available structures of the monomeric forms of the SF1 enzymes bound to ssDNA–dsDNA junctions represent on-pathway intermediates in the DNA-unwinding reaction or autoinhibited complexes is less certain. There is still much to be learned concerning the mechanisms of translocation, duplex unwinding and protein displacement by these enzymes and especially how these activities are regulated by accessory proteins.