登録情報 | データベース: PDB / ID: 2opf |
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タイトル | Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (R252A) in complex with AP-site containing DNA substrate |
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要素 | - 5'-D(*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*G)-3'
- 5'-D(P*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'
- Endonuclease VIII
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キーワード | HYDROLASE/DNA / Endonuclease VIII / oxidative damage / DNA repair / base excision / covalent intermediate / reaction mechanism / HYDROLASE-DNA COMPLEX |
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機能・相同性 | 機能・相同性情報
oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity / 加水分解酵素; 糖加水分解酵素; N-グリコシル化合物加水分解酵素 / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / damaged DNA binding / zinc ion binding類似検索 - 分子機能 Endonuclease VIII / Nei, N-terminal / Zinc finger, DNA glycosylase/AP lyase-type / Zinc finger, FPG/IleRS-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger found in FPG and IleRS / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase H2TH domain ...Endonuclease VIII / Nei, N-terminal / Zinc finger, DNA glycosylase/AP lyase-type / Zinc finger, FPG/IleRS-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger found in FPG and IleRS / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase H2TH domain / N-terminal domain of MutM-like DNA repair proteins / Formamidopyrimidine-DNA glycosylase N-terminal domain / Formamidopyrimidine-DNA glycosylase N-terminal domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase, catalytic domain / Formamidopyrimidine-DNA glycosylase catalytic domain profile. / Formamidopyrimidine-DNA glycosylase H2TH domain / DNA glycosylase/AP lyase, H2TH DNA-binding / Helicase, Ruva Protein; domain 3 - #50 / Helicase, Ruva Protein; domain 3 / Ribosomal protein S13-like, H2TH / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta類似検索 - ドメイン・相同性 |
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生物種 | ![](img/tx_bacteria.gif) Escherichia coli (大腸菌) |
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手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.85 Å |
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データ登録者 | Golan, G. / Zharov, D.O. / Grollman, A.P. / Shoham, G. |
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引用 | ジャーナル: To be Published タイトル: Active site plasticity of endonuclease VIII: Conformational changes compensating for different substrates and mutations of critical residues 著者: Golan, G. / Zharkov, D.O. / Grollman, A.P. / Shoham, G. |
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履歴 | 登録 | 2007年1月29日 | 登録サイト: RCSB / 処理サイト: PDBJ |
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改定 1.0 | 2008年2月26日 | Provider: repository / タイプ: Initial release |
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改定 1.1 | 2011年7月13日 | Group: Non-polymer description / Version format compliance |
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改定 1.2 | 2021年11月10日 | Group: Database references / Derived calculations カテゴリ: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id |
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改定 1.3 | 2023年10月25日 | Group: Data collection / Refinement description カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model |
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