4KYW

Restriction endonuclease DPNI in complex with two DNA molecules

4KYW の概要

• エントリーDOI: 10.2210/pdb4kyw/pdb
• 関連するPDBエントリー: 4ESJ
• 分子名称: Type-2 restriction enzyme DpnI, 5'-(*DC*DTP*DGP*DGP*6MAP*DTP*DCP*DCP*DAP*DG)-3', ZINC ION, ... (6 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: 5
• 化学式量合計: 42442.96

構造登録者

Mierzejewska, K.,Siwek, W.,Czapinska, H.,Skowronek, K.,Bujnicki, J.M.,Bochtler, M. (登録日: 2013-05-29, 公開日: 2014-06-04, 最終更新日: 2023-09-20)

主引用文献

Mierzejewska, K.,Siwek, W.,Czapinska, H.,Kaus-Drobek, M.,Radlinska, M.,Skowronek, K.,Bujnicki, J.M.,Dadlez, M.,Bochtler, M.
Structural basis of the methylation specificity of R.DpnI.
Nucleic Acids Res., 42:8745-8754, 2014

PubMed Abstract: R.DpnI consists of N-terminal catalytic and C-terminal winged helix domains that are separately specific for the Gm6ATC sequences in Dam-methylated DNA. Here we present a crystal structure of R.DpnI with oligoduplexes bound to the catalytic and winged helix domains and identify the catalytic domain residues that are involved in interactions with the substrate methyl groups. We show that these methyl groups in the Gm6ATC target sequence are positioned very close to each other. We further show that the presence of the two methyl groups requires a deviation from B-DNA conformation to avoid steric conflict. The methylation compatible DNA conformation is complementary with binding sites of both R.DpnI domains. This indirect readout of methylation adds to the specificity mediated by direct favorable interactions with the methyl groups and solvation/desolvation effects. We also present hydrogen/deuterium exchange data that support 'crosstalk' between the two domains in the identification of methylated DNA, which should further enhance R.DpnI methylation specificity.

PubMed: 24966351
DOI: 10.1093/nar/gku546

実験手法

X-RAY DIFFRACTION (2.35 Å)