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A sequence-specific DNA glycosylase mediates restriction-modification in Pyrococcus abyssi

Author

Listed:
  • Ken-ichi Miyazono

    (Graduate School of Agricultural and Life Sciences, The University of Tokyo)

  • Yoshikazu Furuta

    (Graduate School of Frontier Science, The University of Tokyo
    Institute of Medical Science, The University of Tokyo)

  • Miki Watanabe-Matsui

    (Graduate School of Frontier Science, The University of Tokyo
    Present address: Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan)

  • Takuya Miyakawa

    (Graduate School of Agricultural and Life Sciences, The University of Tokyo)

  • Tomoko Ito

    (Graduate School of Agricultural and Life Sciences, The University of Tokyo)

  • Ichizo Kobayashi

    (Graduate School of Frontier Science, The University of Tokyo
    Institute of Medical Science, The University of Tokyo
    Graduate Program in Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo)

  • Masaru Tanokura

    (Graduate School of Agricultural and Life Sciences, The University of Tokyo)

Abstract

Restriction-modification systems consist of genes that encode a restriction enzyme and a cognate methyltransferase. Thus far, it was believed that restriction enzymes are sequence-specific endonucleases that introduce double-strand breaks at specific sites by catalysing the cleavages of phosphodiester bonds. Here we report that based on the crystal structure and enzymatic activity, one of the restriction enzymes, R.PabI, is not an endonuclease but a sequence-specific adenine DNA glycosylase. The structure of the R.PabI–DNA complex shows that R.PabI unwinds DNA at a 5′-GTAC-3′ site and flips the guanine and adenine bases out of the DNA helix to recognize the sequence. R.PabI catalyses the hydrolysis of the N-glycosidic bond between the adenine base and the sugar in the DNA and produces two opposing apurinic/apyrimidinic (AP) sites. The opposing AP sites are cleaved by heat-promoted β elimination and/or by endogenous AP endonucleases of host cells to introduce a double-strand break.

Suggested Citation

  • Ken-ichi Miyazono & Yoshikazu Furuta & Miki Watanabe-Matsui & Takuya Miyakawa & Tomoko Ito & Ichizo Kobayashi & Masaru Tanokura, 2014. "A sequence-specific DNA glycosylase mediates restriction-modification in Pyrococcus abyssi," Nature Communications, Nature, vol. 5(1), pages 1-8, May.
    • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms4178
    DOI: 10.1038/ncomms4178
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