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DOI | 10.2210/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 | |
| 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: 21965539DOI: 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) |
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