4ESJ

RESTRICTION ENDONUCLEASE DpnI IN COMPLEX WITH TARGET DNA

4ESJ の概要

• エントリーDOI: 10.2210/pdb4esj/pdb
• 分子名称: Type-2 restriction enzyme DpnI, DNA (5'-D(*CP*TP*GP*GP*(6MA)P*TP*CP*CP*AP*G)-3'), ZINC ION, ... (7 entities in total)
• 機能のキーワード: restriction endonuclease-dna complex, type iim, type iie, restriction enzyme, dpni, methylation dependent, n6-methyladenine, pd-(d/e)xk type endonuclease, winged helix domain, restriction endonuclease, dna binding, hydrolase-dna complex, hydrolase/dna
• 由来する生物種: Streptococcus pneumoniae; 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 72723.18

構造登録者

Siwek, W.,Czapinska, H.,Bochtler, M.,Bujnicki, J.M.,Skowronek, K. (登録日: 2012-04-23, 公開日: 2012-06-13, 最終更新日: 2024-02-28)

主引用文献

Siwek, W.,Czapinska, H.,Bochtler, M.,Bujnicki, J.M.,Skowronek, K.
Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R.DpnI.
Nucleic Acids Res., 40:7563-7572, 2012

PubMed Abstract: DNA methylation-dependent restriction enzymes have many applications in genetic engineering and in the analysis of the epigenetic state of eukaryotic genomes. Nevertheless, high-resolution structures have not yet been reported, and therefore mechanisms of DNA methylation-dependent cleavage are not understood. Here, we present a biochemical analysis and high-resolution DNA co-crystal structure of the N(6)-methyladenine (m6A)-dependent restriction enzyme R.DpnI. Our data show that R.DpnI consists of an N-terminal catalytic PD-(D/E)XK domain and a C-terminal winged helix (wH) domain. Surprisingly, both domains bind DNA in a sequence- and methylation-sensitive manner. The crystal contains R.DpnI with fully methylated target DNA bound to the wH domain, but distant from the catalytic domain. Independent readout of DNA sequence and methylation by the two domains might contribute to R.DpnI specificity or could help the monomeric enzyme to cut the second strand after introducing a nick.

PubMed: 22610857
DOI: 10.1093/nar/gks428

実験手法

X-RAY DIFFRACTION (2.05 Å)