TY - JOUR
T1 - A sequence-specific DNA glycosylase mediates restriction-modification in Pyrococcus abyssi
AU - Miyazono, Ken Ichi
AU - Furuta, Yoshikazu
AU - Watanabe-Matsui, Miki
AU - Miyakawa, Takuya
AU - Ito, Tomoko
AU - Kobayashi, Ichizo
AU - Tanokura, Masaru
N1 - Funding Information:
We thank Hiroshi Ide for discussion. We also thank Ken Furuya, Nobuo Takeda, Atsushi Miyajima, Haruhiko Masaki, Hiroshi Mitani and Sumio Sugano for the arrangement of this manuscript. The synchrotron-radiation experiments were performed at AR-NE3A in the Photon Factory (Tsukuba, Japan) (2008G136 and 2008S2-001). This work was supported by the National Project on Protein Structural and Functional Analyses and the Targeted Proteins Research Program (TPRP) of the Ministry of Education, Culture, Sports, Science and Technology, Japan.
PY - 2014/1/24
Y1 - 2014/1/24
N2 - 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.
AB - 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.
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U2 - 10.1038/ncomms4178
DO - 10.1038/ncomms4178
M3 - Article
C2 - 24458096
AN - SCOPUS:84893121162
VL - 5
JO - Nature Communications
JF - Nature Communications
SN - 2041-1723
M1 - 3178
ER -