Roles for Helicases as ATP-Dependent Molecular Switches

Abstract

On the basis of the familial name, a "helicase" might be expected to have an enzymatic activity that unwinds duplex polynucleotides to form single strands. A more encompassing taxonomy that captures alternative enzymatic roles has defined helicases as a sub-class of molecular motors that move directionally and processively along nucleic acids, the so-called "translocases". However, even this definition may be limiting in capturing the full scope of helicase mechanism and activity. Discussed here is another, alternative view of helicases-as machines which couple NTP-binding and hydrolysis to changes in protein conformation to resolve stable nucleoprotein assembly states. This "molecular switch" role differs from the classical view of helicases as molecular motors in that only a single catalytic NTPase cycle may be involved. This is illustrated using results obtained with the DEAD-box family of RNA helicases and with a model bacterial system, the ATP-dependent Type III restriction-modification enzymes. Further examples are discussed and illustrate the wide-ranging examples of molecular switches in genome metabolism.

DNA cleavage by CgII and NgoAVII requires interaction between N- and R-proteins and extensive nucleotide hydrolysis

“…These values are closer to those reported for Type I restriction enzymes (e.g. EcoR124I ∼998 ATP/s/monomer at 30°C) that use ATP hydrolysis (1–1.5 ATP per bp step) for translocation on intact DNA ( 26 , 31 , 32 ) rather than to those reported for Type III enzymes (∼0.3–0.6 ATP/s/monomer), where ATP hydrolysis is used to drive a molecular switches to activate DNA sliding ( 33 ).…”

“…Helicases use ATP hydrolysis to unwind and/or translocate nucleic acids, and/or to remodel nucleic acids or nucleoprotein complexes ( 15 , 24 , 25 ). The Type I and III RM enzymes both contain domains with SF2 helicase motifs and require ATP hydrolysis for DNA cleavage (see below) ( 26 ). However, the DEAD domains within the N-proteins: have helicase motifs distinct to those found in Type I or III enzymes; are associated with uncharacterized Z1 domains that are not found associated with the helicase domains in Type I or III enzymes ( 14 ); and do not have the nuclease domain fused within a single polypeptide as seen in the HsdR subunits of Type I enzymes and Res subunits of Type III enzymes ( 27 – 29 ).…”

Comparative genomics of defense systems in archaea and bacteria

“…The most complex ATP-dependent Type I R-M systems encompass three genes, which encode the R (restriction), M (modification) and S (specificity) subunits of the R-MA complex; the R subunit also contains a distinct ATPase domain that belongs to the helicase Superfamily II (42,44,45). Type III R-M system resemble Type II systems in that they consist of only R and M subunit but, on the other hand, are similar to Type I systems in that the R subunit also contains the helicase domain and the reaction is ATP-dependent (46,47). Type IV R-M systems are distinct two-subunit complex that consist of a AAA + family GTPase and an endonuclease, and cleave the target DNA non-specifically (45,48).…”

Structural basis of asymmetric DNA methylation and ATP-triggered long-range diffusion by EcoP15I

“…1 ). Together, these results posit a new functionality for helicases, as molecular switches for long-lived DNA sliding (rather than conventional DNA/RNA unwinding or stepwise translocation) 21 . EcoP15I hydrolyses ∼30 ATP molecules in two steps (a fast consumption of ∼10 ATP molecules followed by a slower consumption of ∼20 ATP molecules), which switches the enzyme into a distinct structural state that can diffuse on DNA over long distances 19 .…”