6K1E

Crystal structure of EXD2 exonuclease domain soaked in Mg and GMP

6K1E の概要

• エントリーDOI: 10.2210/pdb6k1e/pdb
• 分子名称: Exonuclease 3'-5' domain-containing protein 2, MAGNESIUM ION (3 entities in total)
• 機能のキーワード: 3'-5' exonuclease, dnaq family, hydrolase
• 由来する生物種: Homo sapiens (Human)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 48889.71

構造登録者

Park, J.,Lee, C. (登録日: 2019-05-10, 公開日: 2019-05-22, 最終更新日: 2023-11-22)

主引用文献

Park, J.,Lee, S.Y.,Jeong, H.,Kang, M.G.,Van Haute, L.,Minczuk, M.,Seo, J.K.,Jun, Y.,Myung, K.,Rhee, H.W.,Lee, C.
The structure of human EXD2 reveals a chimeric 3' to 5' exonuclease domain that discriminates substrates via metal coordination.
Nucleic Acids Res., 47:7078-7093, 2019

PubMed Abstract: EXD2 (3'-5' exonuclease domain-containing protein 2) is an essential protein with a conserved DEDDy superfamily 3'-5' exonuclease domain. Recent research suggests that EXD2 has two potential functions: as a component of the DNA double-strand break repair machinery and as a ribonuclease for the regulation of mitochondrial translation. Herein, electron microscope imaging analysis and proximity labeling revealed that EXD2 is anchored to the mitochondrial outer membrane through a conserved N-terminal transmembrane domain, while the C-terminal region is cytosolic. Crystal structures of the exonuclease domain in complex with Mn2+/Mg2+ revealed a domain-swapped dimer in which the central α5-α7 helices are mutually crossed over, resulting in chimeric active sites. Additionally, the C-terminal segments absent in other DnaQ family exonucleases enclose the central chimeric active sites. Combined structural and biochemical analyses demonstrated that the unusual dimeric organization stabilizes the active site, facilitates discrimination between DNA and RNA substrates based on divalent cation coordination and generates a positively charged groove that binds substrates.

PubMed: 31127291
DOI: 10.1093/nar/gkz454

実験手法

X-RAY DIFFRACTION (2.9 Å)