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Non-hexameric DNA helicases and translocases: mechanisms and regulation

Nature Reviews Molecular Cell Biology volume 9, pages 391–401 (2008)Cite this article

Key Points

  • 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.

Abstract

Helicases and nucleic acid translocases are motor proteins that have essential roles in nearly all aspects of nucleic acid metabolism, ranging from DNA replication to chromatin remodelling. Fuelled by the binding and hydrolysis of nucleoside triphosphates, helicases move along nucleic acid filaments and separate double-stranded DNA into their complementary single strands. Recent evidence indicates that the ability to simply translocate along single-stranded DNA is, in many cases, insufficient for helicase activity. For some of these enzymes, self assembly and/or interactions with accessory proteins seem to regulate their translocase and helicase activities.

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Figure 1: Multiple activities of SF1 and SF2 helicases and translocases.
Figure 2: Domain structure and domain movement of superfamily-1 translocase and helicase monomers.
Figure 3: Potential mechanisms of the regulation of multiple SF1 helicase/translocase activities.

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Acknowledgements

We thank the members of the Lohman laboratory as well as A. Lucius, R. Galletto, N. K. Maluf, C. Fischer, A. Pyle and J. Carey for discussions and comments. The authors of this work are supported by a National Institutes of Health (NIH) grant.

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  1. Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, 63110, Missouri, USA

    Timothy M. Lohman, Eric J. Tomko & Colin G. Wu

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  1. Timothy M. Lohman
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  2. Eric J. Tomko
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Correspondence to Timothy M. Lohman.

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DATABASES

UniProtKB 

PcrA

Rep

UvrD

RecG

RecQ

VASA

Hel308

RecB

RecD

RecC

Srs2

FURTHER INFORMATION

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Glossary

Holliday junction

A cruciform DNA structure that is generated during the synaptic phase of homologous recombination.

RNA DEAD-box helicase

An enzyme that unwinds RNA duplexes and contains the evolutionarily conserved motif DEAD (Asp-Glu-Ala-Asp) in the helicase core region.

Ensemble study

An experiment performed with a large population of molecules and during which the average behaviour of the population is monitored.

Kinesin

A microtubule-based molecular motor, most often directed towards the plus end of microtubules.

Myosin

A molecular motor that moves along actin filaments and has several cellular roles in contraction or protein transport.

FRET

(Fluorescence resonance energy transfer). The transfer of energy between a donor and an acceptor fluorophore when the donor is directly excited with one wavelength of light. The acceptor then re-emits the energy with a different, longer wavelength that is characteristic of the acceptor fluorophore. Transfer only occurs if the two fluorophores are within a characteristic distance that depends on the spectral properties of the donor and acceptor.

AMPPNP

A non-hydrolysable ATP analogue.

Replication fork

A site in double-stranded DNA where the template strands are separated, allowing a newly formed copy of the DNA to be synthesized. The fork moves in the direction of leading-strand synthesis.

Telomeric DNA end

A segment at the end of a chromosome arm that consists of a series of repeated DNA sequences.

Crossover hotspot instigator sequence

(Chi sequence). A specific nucleotide sequence (5′-GCTGGTGG-3′) that facilitates the nearby occurrence of recombination and crossing over.

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Lohman, T., Tomko, E. & Wu, C. Non-hexameric DNA helicases and translocases: mechanisms and regulation. Nat Rev Mol Cell Biol 9, 391–401 (2008). https://doi.org/10.1038/nrm2394

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