Three-dimensional structure of a DNA repair enzyme, 3-methyladenine DNA glycosylase II, from Escherichia coli

Yuriko Yamagata; Masato Kato; Kyoko Odawara; Yoshiteru Tokuno; Yoko Nakashima; Nobuko Matsushima; Kohei Yasumura; Ken Ichi Tomita; Kenji Ihara; Yoshimitsu Fujii; Yusaku Nakabeppu; Mutsuo Sekiguchi; Satoshi Fujii

doi:10.1016/S0092-8674(00)80102-6

Three-dimensional structure of a DNA repair enzyme, 3-methyladenine DNA glycosylase II, from Escherichia coli

Yuriko Yamagata, Masato Kato, Kyoko Odawara, Yoshiteru Tokuno, Yoko Nakashima, Nobuko Matsushima, Kohei Yasumura, Ken Ichi Tomita, Kenji Ihara, Yoshimitsu Fujii, Yusaku Nakabeppu, Mutsuo Sekiguchi, Satoshi Fujii

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Abstract

The three-dimensional structure of Escherichia coli 3-methyladenine DNA glycosylase II, which removes numerous alkylated bases from DNA, was solved at 2.3 Å resolution. The enzyme consists of three domains: one α + β fold domain with a similarity to one-half of the eukaryotic TATA box-binding protein, and two all α-helical domains similar to those of Escherichia coli endonuclease III with combined N-glycosylase/abasic lyase activity. Mutagenesis and model-building studies suggest that the active site is located in a cleft between the two helical domains and that the enzyme flips the target base out of the DNA duplex into the active-site cleft. The structure of the active site implies broad substrate specificity and simple N-glycosylase activity.

Original language	English (US)
Pages (from-to)	311-319
Number of pages	9
Journal	Cell
Volume	86
Issue number	2
DOIs	https://doi.org/10.1016/S0092-8674(00)80102-6
State	Published - Jul 26 1996

ASJC Scopus subject areas

Biochemistry, Genetics and Molecular Biology(all)

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10.1016/S0092-8674(00)80102-6

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@article{f13592420bd745f0b1874c8cd4523696,

title = "Three-dimensional structure of a DNA repair enzyme, 3-methyladenine DNA glycosylase II, from Escherichia coli",

abstract = "The three-dimensional structure of Escherichia coli 3-methyladenine DNA glycosylase II, which removes numerous alkylated bases from DNA, was solved at 2.3 {\AA} resolution. The enzyme consists of three domains: one α + β fold domain with a similarity to one-half of the eukaryotic TATA box-binding protein, and two all α-helical domains similar to those of Escherichia coli endonuclease III with combined N-glycosylase/abasic lyase activity. Mutagenesis and model-building studies suggest that the active site is located in a cleft between the two helical domains and that the enzyme flips the target base out of the DNA duplex into the active-site cleft. The structure of the active site implies broad substrate specificity and simple N-glycosylase activity.",

author = "Yuriko Yamagata and Masato Kato and Kyoko Odawara and Yoshiteru Tokuno and Yoko Nakashima and Nobuko Matsushima and Kohei Yasumura and Tomita, {Ken Ichi} and Kenji Ihara and Yoshimitsu Fujii and Yusaku Nakabeppu and Mutsuo Sekiguchi and Satoshi Fujii",

note = "Funding Information: Correspondence should be addressed to Y. Y. We thank Dr. K. Yutani for the use of graphics facilities and the staff of the Research Center for Protein Engineering, Institute for Protein Research, Osaka University, for the use of NEC engineering workstations. This work was supported by a Grant-in-Aid for Scientific Research from the Ministry of Education, Science, and Culture of Japan; the Hayashi Memorial Foundation for Female Natural Scientists; and TARA (Tsukuba Advanced Research Alliance)–Sakabe Project.",

year = "1996",

month = jul,

day = "26",

doi = "10.1016/S0092-8674(00)80102-6",

language = "English (US)",

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pages = "311--319",

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T1 - Three-dimensional structure of a DNA repair enzyme, 3-methyladenine DNA glycosylase II, from Escherichia coli

AU - Yamagata, Yuriko

AU - Kato, Masato

AU - Odawara, Kyoko

AU - Tokuno, Yoshiteru

AU - Nakashima, Yoko

AU - Matsushima, Nobuko

AU - Yasumura, Kohei

AU - Tomita, Ken Ichi

AU - Ihara, Kenji

AU - Fujii, Yoshimitsu

AU - Nakabeppu, Yusaku

AU - Sekiguchi, Mutsuo

AU - Fujii, Satoshi

N1 - Funding Information: Correspondence should be addressed to Y. Y. We thank Dr. K. Yutani for the use of graphics facilities and the staff of the Research Center for Protein Engineering, Institute for Protein Research, Osaka University, for the use of NEC engineering workstations. This work was supported by a Grant-in-Aid for Scientific Research from the Ministry of Education, Science, and Culture of Japan; the Hayashi Memorial Foundation for Female Natural Scientists; and TARA (Tsukuba Advanced Research Alliance)–Sakabe Project.

PY - 1996/7/26

Y1 - 1996/7/26

N2 - The three-dimensional structure of Escherichia coli 3-methyladenine DNA glycosylase II, which removes numerous alkylated bases from DNA, was solved at 2.3 Å resolution. The enzyme consists of three domains: one α + β fold domain with a similarity to one-half of the eukaryotic TATA box-binding protein, and two all α-helical domains similar to those of Escherichia coli endonuclease III with combined N-glycosylase/abasic lyase activity. Mutagenesis and model-building studies suggest that the active site is located in a cleft between the two helical domains and that the enzyme flips the target base out of the DNA duplex into the active-site cleft. The structure of the active site implies broad substrate specificity and simple N-glycosylase activity.

AB - The three-dimensional structure of Escherichia coli 3-methyladenine DNA glycosylase II, which removes numerous alkylated bases from DNA, was solved at 2.3 Å resolution. The enzyme consists of three domains: one α + β fold domain with a similarity to one-half of the eukaryotic TATA box-binding protein, and two all α-helical domains similar to those of Escherichia coli endonuclease III with combined N-glycosylase/abasic lyase activity. Mutagenesis and model-building studies suggest that the active site is located in a cleft between the two helical domains and that the enzyme flips the target base out of the DNA duplex into the active-site cleft. The structure of the active site implies broad substrate specificity and simple N-glycosylase activity.

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Three-dimensional structure of a DNA repair enzyme, 3-methyladenine DNA glycosylase II, from Escherichia coli

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