3ZDC

Structure of E. coli ExoIX in complex with the palindromic 5ov4 DNA oligonucleotide, potassium and calcium

3ZDC の概要

• エントリーDOI: 10.2210/pdb3zdc/pdb
• 関連するPDBエントリー: 3ZD8 3ZD9 3ZDA 3ZDB 3ZDD 3ZDE
• 分子名称: PROTEIN XNI, 5OV4 DNA, 5'-D(*AP*AP*AP*AP*GP*CP*GP*TP*AP*CP*GP*CP)-3', POTASSIUM ION, ... (6 entities in total)
• 機能のキーワード: hydrolase, exoix, flap endonuclease, dna binding
• 由来する生物種: ESCHERICHIA COLI; 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 32120.93

構造登録者

Hemsworth, G.R.,Anstey-Gilbert, C.S.,Flemming, C.S.,Hodskinson, M.R.G.,Zhang, J.,Sedelnikova, S.E.,Stillman, T.J.,Sayers, J.R.,Artymiuk, P.J. (登録日: 2012-11-26, 公開日: 2013-07-10, 最終更新日: 2025-12-10)

主引用文献

Anstey-Gilbert, C.S.,Hemsworth, G.R.,Flemming, C.S.,Hodskinson, M.R.G.,Zhang, J.,Sedelnikova, S.E.,Stillman, T.J.,Sayers, J.R.,Artymiuk, P.J.
The Structure of E. Coli Exoix - Implications for DNA Binding and Catalysis in Flap Endonucleases
Nucleic Acids Res., 41:8357-, 2013

PubMed Abstract: Escherichia coli Exonuclease IX (ExoIX), encoded by the xni gene, was the first identified member of a novel subfamily of ubiquitous flap endonucleases (FENs), which possess only one of the two catalytic metal-binding sites characteristic of other FENs. We have solved the first structure of one of these enzymes, that of ExoIX itself, at high resolution in DNA-bound and DNA-free forms. In the enzyme-DNA cocrystal, the single catalytic site binds two magnesium ions. The structures also reveal a binding site in the C-terminal domain where a potassium ion is directly coordinated by five main chain carbonyl groups, and we show this site is essential for DNA binding. This site resembles structurally and functionally the potassium sites in the human FEN1 and exonuclease 1 enzymes. Fluorescence anisotropy measurements and the crystal structures of the ExoIX:DNA complexes show that this potassium ion interacts directly with a phosphate diester in the substrate DNA.

PubMed: 23821668
DOI: 10.1093/NAR/GKT591

実験手法

X-RAY DIFFRACTION (1.53 Å)