Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

RecBCD enzyme is a DNA helicase with fast and slow motors of opposite polarity


Helicases are molecular motors that move along and unwind double-stranded nucleic acids1. RecBCD enzyme is a complex helicase and nuclease, essential for the major pathway of homologous recombination and DNA repair in Escherichia coli2. It has sets of helicase motifs1 in both RecB and RecD, two of its three subunits. This rapid, highly processive enzyme unwinds DNA in an unusual manner: the 5′-ended strand forms a long single-stranded tail, whereas the 3′-ended strand forms an ever-growing single-stranded loop and short single-stranded tail. Here we show by electron microscopy of individual molecules that RecD is a fast helicase acting on the 5′-ended strand and RecB is a slow helicase acting on the 3′-ended strand on which the single-stranded loop accumulates. Mutational inactivation of the helicase domain in RecB or in RecD, or removal of the RecD subunit, altered the rates of unwinding or the types of structure produced, or both. This dual-helicase mechanism explains how the looped recombination intermediates are generated and may serve as a general model for highly processive travelling machines with two active motors, such as other helicases and kinesins.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: RecBK29QCD enzyme, with an inactive RecB helicase, unwinds DNA by means of a loop and a 5′-terminated tail.
Figure 2: Enzymes without RecD or with mutant RecD (RecBCDK177Q) unwind DNA slowly and with different topologies.
Figure 3: Analysis of DNA unwinding by RecBCD and RecBCDK177Q.
Figure 4: Model for unwinding by RecBCD enzyme.


  1. Lohman, T. M. & Bjornson, K. P. Mechanisms of helicase-catalyzed DNA unwinding. Annu. Rev. Biochem. 65, 169–214 (1996)

    Article  CAS  Google Scholar 

  2. Smith, G. R. Homologous recombination near and far from DNA breaks: Alternative roles and contrasting views. Annu. Rev. Genet. 35, 243–274 (2001)

    Article  CAS  Google Scholar 

  3. Taylor, A. & Smith, G. R. Unwinding and rewinding of DNA by the RecBC enzyme. Cell 22, 447–457 (1980)

    Article  CAS  Google Scholar 

  4. Velankar, S. S., Soultanas, P., Dillingham, M. S., Subramaya, H. S. & Wigley, D. B. Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism. Cell 97, 75–84 (1999)

    Article  CAS  Google Scholar 

  5. Phillips, R. J., Hickleton, D. C., Boehmer, P. E. & Emmerson, P. T. The RecB protein of Escherichia coli translocates along single-stranded DNA in the 3′ to 5′ direction: a proposed ratchet mechanism. Mol. Gen. Genet. 254, 319–329 (1997)

    CAS  PubMed  Google Scholar 

  6. Chen, H.-W., Ruan, B., Yu, M., Wang, J.-d & Julin, D. A. The RecD subunit of the RecBCD enzyme from Escherichia coli is a single-stranded DNA dependent ATPase. J. Biol. Chem. 272, 10072–10079 (1997)

    Article  CAS  Google Scholar 

  7. Dillingham, M. S., Spies, M. & Kowalczykowski, S. C. RecBCD enzyme is a bipolar DNA helicase. Nature 423, 893–897 (2003)

    Article  ADS  CAS  Google Scholar 

  8. Chen, H.-W., Randle, D. E., Gabbidon, M. & Julin, D. A. Functions of the ATP hydrolysis subunits (RecB and RecD) in the nuclease reactions catalyzed by the RecBCD enzyme from Escherichia coli. J. Mol. Biol. 278, 89–104 (1998)

    Article  CAS  Google Scholar 

  9. Sarasante, M., Sibbold, P. R. & Wittinghofer, A. The P-loop—a common motif in ATP- and GTP-binding proteins. Trends Biochem. Sci. 15, 430–434 (1990)

    Article  Google Scholar 

  10. George, J. W., Brosh, R. M. Jr & Matson, S. W. A dominant negative allele of the Escherichia coli uvrD gene encoding DNA helicase II. A biochemical and genetic characterization. J. Mol. Biol. 229, 67–78 (1994)

    Google Scholar 

  11. Taylor, A. F. & Smith, G. R. Monomeric RecBCD enzyme binds and unwinds DNA. J. Biol. Chem. 270, 24451–24458 (1995)

    Article  CAS  Google Scholar 

  12. Braedt, G. & Smith, G. R. Strand specificity of DNA unwinding by RecBCD enzyme. Proc. Natl Acad. Sci. USA 86, 871–875 (1989)

    Article  ADS  CAS  Google Scholar 

  13. Korangy, F. & Julin, D. A. Efficiency of ATP hydrolysis and DNA unwinding by the RecBC enzyme from Escherichia coli. Biochemistry 33, 9552–9560 (1994)

    Article  CAS  Google Scholar 

  14. Masterson, C. et al. Reconstitution of the activities of the RecBCD holoenzyme of Escherichia coli from the purified subunits. J. Biol. Chem. 267, 13564–13572 (1992)

    CAS  PubMed  Google Scholar 

  15. Dohoney, K. M. & Gelles, J. χ-sequence recognition and DNA translocation by single RecBCD helicase/nuclease molecules. Nature 409, 370–374 (2001)

    Article  ADS  CAS  Google Scholar 

  16. Bianco, P. R. et al. Processive translocation and DNA unwinding by individual RecBCD enzyme molecules. Nature 409, 374–378 (2001)

    Article  ADS  CAS  Google Scholar 

  17. Dillingham, M. S., Wigley, D. B. & Webb, M. R. Direct measurements of single-stranded DNA translocation by PcrA helicase using the fluorescent base analogue 2-aminopurine. Biochemistry 41, 643–651 (2002)

    Article  CAS  Google Scholar 

  18. Lee, M. S. & Marians, K. J. Differential ATP requirements distinguish the DNA translocation and DNA unwinding activities of the Escherichia coli PRI A protein. J. Biol. Chem. 265, 17078–17083 (1990)

    CAS  PubMed  Google Scholar 

  19. Ganesan, S. & Smith, G. R. Strand-specific binding to duplex DNA ends by the subunits of Escherichia coli RecBCD enzyme. J. Mol. Biol. 229, 67–78 (1992)

    Article  Google Scholar 

  20. Chaudhury, A. M. & Smith, G. R. A new class of Escherichia coli recBC mutants: Implications for the role of RecBC enzyme in homologous recombination. Proc. Natl Acad. Sci. USA 81, 7850–7854 (1984)

    Article  ADS  CAS  Google Scholar 

  21. Yu, M., Souaya, J. & Julin, D. A. Identification of the nuclease active site in the multifunctional RecBCD enzyme by creation of a chimeric enzyme. J. Mol. Biol. 283, 797–808 (1998)

    Article  CAS  Google Scholar 

  22. Korangy, F. & Julin, D. A. Enzymatic effects of a lysine-to-glutamine mutation in the ATP-binding consensus sequence in the RecD subunit of the RecBCD enzyme from Escherichia coli. J. Biol. Chem. 267, 1733–1740 (1992)

    CAS  PubMed  Google Scholar 

  23. Hsieh, S. & Julin, D. A. Alteration by site-directed mutagenesis of the conserved lysine residue in the consensus ATP-binding sequence of the RecB protein of Escherichia coli. Nucleic Acids Res. 20, 5647–5653 (1992)

    Article  CAS  Google Scholar 

  24. Anderson, D. G. & Kowalczykowski, S. C. The recombination hot spot χ is a regulatory element that switches the polarity of DNA degradation by the RecBCD enzyme. Genes Dev. 11, 571–581 (1997)

    Article  CAS  Google Scholar 

  25. Bianco, P. R. & Kowalczykowski, S. C. The recombination hotspot χ is recognized by the translocating RecBCD enzyme as the single strand of DNA containing the sequence 5′-GCTGGTGG-3′. Proc. Natl Acad. Sci. USA 94, 6706–6711 (1997)

    Article  ADS  CAS  Google Scholar 

  26. Anderson, D. G. & Kowalczykowski, S. C. The translocating RecBCD enzyme stimulates recombination by directing RecA protein onto ssDNA in a χ-regulated manner. Cell 90, 77–86 (1997)

    Article  CAS  Google Scholar 

  27. Tomishige, M., Klopfenstein, D. R. & Vale, R. D. Conversion of Unc104/KIF1A kinesin into a processive motor after dimerization. Science 297, 2263–2267 (2002)

    Article  ADS  CAS  Google Scholar 

  28. Ha, T. et al. Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase. Nature 419, 638–641 (2002)

    Article  ADS  CAS  Google Scholar 

  29. Berneburg, M. & Lehmann, A. R. Xeroderma pigmentosum and related disorders: defects in DNA repair and transcription. Adv. Genet. 43, 71–102 (2001)

    Article  CAS  Google Scholar 

  30. Boehmer, P. E. & Emmerson, P. T. Escherichia coli RecBCD enzyme: inducible overproduction and reconstitution of the ATP-dependent deoxyribonuclease from purified subunits. Gene 102, 1–6 (1991)

    Article  CAS  Google Scholar 

Download references


We thank D. Julin for advice on protein purification; M. Dillingham, M. Spies and S. Kowalczykowski for sharing their unpublished information7; S. Amundsen for permission to cite unpublished results; J. Cooper, M. Gellert, N. Maizels, R. Strong and our colleagues for comments on the manuscript; and L. Caldwell and staff for help with the electron microscopy. This research was supported by grants from the NIH.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Gerald R. Smith.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Taylor, A., Smith, G. RecBCD enzyme is a DNA helicase with fast and slow motors of opposite polarity. Nature 423, 889–893 (2003).

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI:

This article is cited by


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing