1M0D

Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site and Bound Manganese Ions

1M0D の概要

• エントリーDOI: 10.2210/pdb1m0d/pdb
• 関連するPDBエントリー: 1FZR 1M0I
• 分子名称: Endodeoxyribonuclease I, MANGANESE (II) ION, SULFATE ION, ... (4 entities in total)
• 機能のキーワード: holliday junction resolvase, homodimer, domain swapped, composite active site, hydrolase
• 由来する生物種: Enterobacteria phage T7
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 65101.72

構造登録者

Hadden, J.M.,Declais, A.C.,Phillips, S.E.,Lilley, D.M. (登録日: 2002-06-12, 公開日: 2002-07-10, 最終更新日: 2024-02-14)

主引用文献

Hadden, J.M.,Declais, A.C.,Phillips, S.E.,Lilley, D.M.
Metal ions bound at the active site of the junction-resolving enzyme T7 endonuclease I.
EMBO J., 21:3505-3515, 2002

PubMed Abstract: T7 endonuclease I is a nuclease that is selective for the structure of the four-way DNA junction. The active site is similar to those of a number of restriction enzymes. We have solved the crystal structure of endonuclease I with a wild-type active site. Diffusion of manganese ions into the crystal revealed two peaks of electron density per active site, defining two metal ion-binding sites. Site 1 is fully occupied, and the manganese ion is coordinated by the carboxylate groups of Asp55 and Glu65, and the main chain carbonyl of Thr66. Site 2 is partially occupied, and the metal ion has a single protein ligand, the remaining carboxylate oxygen atom of Asp55. Isothermal titration calorimetry showed the sequential exothermic binding of two manganese ions in solution, with dissociation constants of 0.58 +/- 0.019 and 14 +/- 1.5 mM. These results are consistent with a two metal ion mechanism for the cleavage reaction, in which the hydrolytic water molecule is contained in the first coordination sphere of the site 1-bound metal ion.

PubMed: 12093751
DOI: 10.1093/emboj/cdf337

実験手法

X-RAY DIFFRACTION (1.9 Å)