6GCF

DNA binding domain of restriction endonuclease McrBC in complex with N4-methylcytosine DNA

6GCF の概要

• エントリーDOI: 10.2210/pdb6gcf/pdb
• 関連するPDBエントリー: 6GCD 6GCE
• 分子名称: 5-methylcytosine-specific restriction enzyme B, DNA (5'-D(*GP*AP*GP*AP*CP*CP*GP*GP*TP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*AP*(C34)P*CP*GP*GP*TP*CP*TP*C)-3'), ... (4 entities in total)
• 機能のキーワード: n4-methylcytosine, restriction endonuclease, mcrbc, base flipping, dna binding protein
• 由来する生物種: Escherichia coli; 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 46660.65

構造登録者

Sasnauskas, G. (登録日: 2018-04-17, 公開日: 2018-09-19, 最終更新日: 2024-01-17)

主引用文献

Zagorskaite, E.,Manakova, E.,Sasnauskas, G.
Recognition of modified cytosine variants by the DNA-binding domain of methyl-directed endonuclease McrBC.
FEBS Lett., 592:3335-3345, 2018

PubMed Abstract: Cytosine modifications expand the information content of genomic DNA in both eukaryotes and prokaryotes, providing means for epigenetic regulation and self versus nonself discrimination. For example, the methyl-directed restriction endonuclease, McrBC, recognizes and cuts invading bacteriophage DNA containing 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), and N4-methylcytosine (4mC), leaving the unmodified host DNA intact. Here, we present cocrystal structures of McrB-N bound to DNA oligoduplexes containing 5hmC, 5-formylcytosine (5fC), and 4mC, and characterize the relative affinity of McrB-N to various cytosine variants. We find that McrB-N flips out modified bases into a protein pocket and binds cytosine derivatives in the order of descending affinity: 4mC > 5mC > 5hmC ≫ 5fC. We also show that pocket mutations alter the relative preference of McrB-N to 5mC, 5hmC, and 4mC.

PubMed: 30194838
DOI: 10.1002/1873-3468.13244

実験手法

X-RAY DIFFRACTION (1.55 Å)