4UT0

THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 10 DAYS INCUBATION IN 5MM MN (STATE 7)

4UT0 の概要

• エントリーDOI: 10.2210/pdb4ut0/pdb
• 分子名称: HOMING ENDONUCLEASE I-DMOI, 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3', 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3', ... (8 entities in total)
• 機能のキーワード: hydrolase-dna complex, catalysis, protein-dna interaction, hydrolase/dna
• 由来する生物種: DESULFUROCOCCUS MOBILIS; 詳細
• タンパク質・核酸の鎖数: 15
• 化学式量合計: 116120.76

構造登録者

Molina, R.,Stella, S.,Redondo, P.,Gomez, H.,Marcaida, M.J.,Orozco, M.,Prieto, J.,Montoya, G. (登録日: 2014-07-17, 公開日: 2014-12-17, 最終更新日: 2024-01-10)

主引用文献

Molina, R.,Stella, S.,Redondo, P.,Gomez, H.,Marcaida, M.J.,Orozco, M.,Prieto, J.,Montoya, G.
Visualizing Phosphodiester-Bond Hydrolysis by an Endonuclease.
Nat.Struct.Mol.Biol., 22:65-, 2015

PubMed Abstract: The enzymatic hydrolysis of DNA phosphodiester bonds has been widely studied, but the chemical reaction has not yet been observed. Here we follow the generation of a DNA double-strand break (DSB) by the Desulfurococcus mobilis homing endonuclease I-DmoI, trapping sequential stages of a two-metal-ion cleavage mechanism. We captured intermediates of the different catalytic steps, and this allowed us to watch the reaction by 'freezing' multiple states. We observed the successive entry of two metals involved in the reaction and the arrival of a third cation in a central position of the active site. This third metal ion has a crucial role, triggering the consecutive hydrolysis of the targeted phosphodiester bonds in the DNA strands and leaving its position once the DSB is generated. The multiple structures show the orchestrated conformational changes in the protein residues, nucleotides and metals during catalysis.

PubMed: 25486305
DOI: 10.1038/NSMB.2932

実験手法

X-RAY DIFFRACTION (2.4 Å)