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3TA7

Zinc bound structure of an archaeal member of the LigD 3'-phosphoesterase DNA repair enzyme family

3TA7 の概要
エントリーDOI10.2210/pdb3ta7/pdb
関連するPDBエントリー3P4H 3TA5
分子名称ATP-dependent DNA ligase, N-terminal domain protein, ZINC ION, PHOSPHATE ION, ... (5 entities in total)
機能のキーワード3'-phosphoesterase, hydrolase
由来する生物種Candidatus Korarchaeum cryptofilum OPF8
タンパク質・核酸の鎖数1
化学式量合計14116.60
構造登録者
Das, U.,Smith, P.,Shuman, S. (登録日: 2011-08-03, 公開日: 2011-10-12, 最終更新日: 2024-02-28)
主引用文献Das, U.,Smith, P.,Shuman, S.
Structural insights to the metal specificity of an archaeal member of the LigD 3'-phosphoesterase DNA repair enzyme family.
Nucleic Acids Res., 40:828-836, 2012
Cited by
PubMed Abstract: LigD 3'-phosphoesterase (PE) enzymes perform end-healing reactions at DNA breaks. Here we characterize the 3'-ribonucleoside-resecting activity of Candidatus Korarchaeum PE. CkoPE prefers a single-stranded substrate versus a primer-template. Activity is abolished by vanadate (10 mM), but is less sensitive to phosphate (IC(50) 50 mM) or chloride (IC(50) 150 mM). The metal requirement is satisfied by manganese, cobalt, copper or cadmium, but not magnesium, calcium, nickel or zinc. Insights to CkoPE metal specificity were gained by solving new 1.5 Å crystal structures of CkoPE in complexes with Co(2+) and Zn(2+). His9, His15 and Asp17 coordinate cobalt in an octahedral complex that includes a phosphate anion, which is in turn coordinated by Arg19 and His51. The cobalt and phosphate positions and the atomic contacts in the active site are virtually identical to those in the CkoPE·Mn(2+) structure. By contrast, Zn(2+) binds in the active site in a tetrahedral complex, wherein the position, orientation and atomic contacts of the phosphate are shifted and its interaction with His51 is lost. We conclude that: (i) PE selectively binds to 'soft' metals in either productive or non-productive modes and (ii) PE catalysis depends acutely on proper metal and scissile phosphate geometry.
PubMed: 21965539
DOI: 10.1093/nar/gkr767
主引用文献が同じPDBエントリー
実験手法
X-RAY DIFFRACTION (1.48 Å)
構造検証レポート
Validation report summary of 3ta7
検証レポート(詳細版)ダウンロードをダウンロード

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件を2026-02-04に公開中

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