DNA Helicases

Abstract

Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) helicases are organised into six SuperFamilies (SF) of enzymes using sequence alignments, biochemical data and available crystal structures. DNA helicases, members of which are found in each of the SF, are an essential group of motor proteins that unwind DNA duplexes into their component single strands in a process that is coupled to the hydrolysis of nucleoside 5′‐triphosphates (NTPs). These enzymes share common biochemical properties that include the binding of single‐ and double‐stranded DNA, NTP binding and hydrolysis, and NTP hydrolysis‐coupled, polar unwinding of duplex DNA. DNA helicases participate in every aspect of DNA metabolism due to the requirement for transient separation of small regions of the duplex genome into its component strands so that replication, recombination and repair can occur.

Key Concepts:

  • DNA helicases unwind duplex DNA in catalytic fashion.

  • DNA helicases translocate unidirectionally in polar fashion.

  • Helicases hydrolyse nucleoside triphosphates.

  • DNA helicases are critical to all aspects of DNA metabolism.

  • There are two broad classes of DNA helicases: hexameric and nonhexameric.

Keywords: recombination; ATPases; protein–DNA complexes; hexameric rings; DNA unwinding

Figure 1.

DNA helicases can have different oligomeric states to achieve DNA unwinding. (a) The E. coli UvrD enzyme is active as a monomer. The helicase (dark blue) is shown bound to a tailed DNA molecule (orange). An ATP analogue (yellow) is shown bound between the two RecA‐like domains. Adapted from Lee and Yang . The arrow indicates the direction of translocation and DNA unwinding. (b) The E. coli RuvAB branch migration complex is shown bound to a Holliday Junction (purple). The RuvA tetramer (green) binds to the junction and is flanked by two diametrically opposed RuvB hexamers (orange). The horizontal arrows indicate the direction of DNA pumping by the RuvB hexamers onto the surface of RuvA where strand separation occurs. Vertical arrows show the direction of movement of nascent heteroduplex DNA as it is pumped off the surface of RuvA. The arrows labelled ‘X’ indicate the acidic pins used to separate the strands of the DNA duplex. The images is adapted from Yamada et al., with coordinates supplied by K. Yamada.

Figure 2.

The DNA follows different paths during DNA unwinding by nonhexameric DNA helicases. (a) The UvrD monomer. The enzyme is shown as a ribbon (dark blue) bound to a tailed DNA molecule (cyan and yellow). One strand of the duplex is forced through the interior of the enzyme whereas the displaced strand is forced to the outside (dashed cyan line). The ATP binding pocket is highlighted in light green with an ATP analogue bound (red). This region is highlighted so that the close positioning to the DNA can be visualised. Adapted from Lee and Yang . (b–d) The three‐subunit E. coli RecBCD enzyme. (b) The enzyme is viewed from the side bound to DNA (orange). The leading domain of RecB can be seen reaching out ahead of the body of the enzyme to pull the duplex DNA into the complex where it is unwound. (c) The same side view of the enzyme but with the RecD subunit removed. In this view, the unwound single strand of DNA can be seen exiting a channel in the RecC subunit. It is also apparent from this view, how intimately associated with one another the RecB and RecC subunits are. (d) RecBCD viewed from the bottom. In this image, the DNA is coloured black and the RecB and C subunits are transparent so that the path of the DNA through the enzyme can be easily seen. Adapted from Saikrishnan et al. and Singleton et al.. For all images, the direction of translocation and DNA unwinding is from right to left.

Figure 3.

Models for DNA unwinding catalysed by hexameric DNA helicases. (a) The bacteriophage T7 gp4A′ replicative helicase (Yu et al., ). A hexameric ring encircles only single‐stranded DNA, which is bound in the central channel to one or two subunits. The second (3′) strand is displaced to the outside of the torus. For gp4 to function in vitro, there must exist a noncomplementary 3′ tail, which allows for the initial displacement of the second strand. Energy from ATP hydrolysis is used to translocate the hexamer along the single‐stranded DNA in a 5′ to 3′ direction (gp4 is a 5′‐to‐3′ helicase). This model is consistent with the observation that a bulky adduct placed in the double‐stranded DNA on the strand labelled 3′ has no effect on helicase activity, whereas the same adduct placed in the double‐stranded region on the strand labelled 5′ inhibits helicase activity (Yong and Romano, ). This model is also supported by other biochemical observations (Hacker and Johnson, ). (b) The SV40 large T‐antigen. The enzyme is viewed from the bottom so that the central hole is visible as are the six bound ADP molecules (yellow). As many hexameric helicases function as a trimer of dimers, the subunits are coloured in dark/light green, blue and brown indicating the three dimers. Images are adapted from Li et al.. (c). RuvB encircles duplex DNA. In contrast to T7 gp4A′ and large T‐antigen which encircle only one strand of the duplex, RuvB encircles both strands (blue). This DNA molecule is pumped intact onto the surface of RuvA where strand separation occurs (pumping is in the direction of the arrow). (d) The RuvB hexamer viewed from the bottom. The central channel is clearly visible and the diameter of the channel is greater than that of SV40 large T‐antigen (panel B). As RuvB acts as a trimer of dimers, dimer pairs are coloured light/dark with bound ATP coloured in fuchsia.

Figure 4.

The quantum inchworm mechanism for DNA unwinding by a nonhexameric DNA helicase. This model is adapted from a study of the E. coli RecBC enzyme (Bianco and Kowalczykowski, ). A single catalytic cycle of translocation and DNA unwinding is shown. The individual strands of the DNA duplex are coloured red (3′‐terminated strand) and blue (5′‐terminated strand). Translocation is from right to left along only one strand of the duplex. The enzyme contains two domains: a leading domain (L; black, which anchors the enzyme to only one strand of duplex DNA) and a trailing domain (T; grey, responsible for DNA unwinding). In stage 1, the enzyme is shown bound to the end of the DNA with the leading domain primed to initiate the reaction (yellow hands). Stages 2–4, the leading domain anchors the enzyme via the two hands (green). The trailing domain translocates along the 3′‐terminated strand toward the leading domain. The curved green arrow indicates movement of the trailing domain; the dashed line indicates the starting position of the domain before movement occurred. As the trailing domain approaches the anchored leading domain, a signal is passed from the lagging to the leading domain. This induces stress in the leading domain (red hands, stage 5), causing it to release and rebind 23 nt ahead, resetting the helicase for another catalytic cycle (stage 6). During this single cycle, only 5 ATP molecules are shown for clarity. In reality, as many as 15 may bind and be hydrolysed (Bianco and Kowalczykowski, ).

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Further Reading

Patel SS and Picha KM (2000) Structure and function of hexameric helicases. Annual Review of Biochemistry 69: 651–697.

Sun B, Johnson DS, Patel G et al. (2011) ATP‐induced helicase slippage reveals highly coordinated subunits. Nature 478(7367): 132–135.

Yodh JG, Schlierf M and Ha T (2010) Insight into helicase mechanism and function revealed through single‐molecule approaches. Quarterly Reviews of Biophysics 43(2): 185–217.

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How to Cite close
Bianco, Piero R(Feb 2012) DNA Helicases. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001046.pub2]