4QEP

crystal structure of KRYPTONITE in complex with mCHG DNA and SAH

4QEP の概要

• エントリーDOI: 10.2210/pdb4qep/pdb
• 関連するPDBエントリー: 4QEN 4QEO
• 分子名称: Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4, DNA (5'-D(*GP*GP*TP*AP*CP*TP*(5CM)P*AP*GP*CP*AP*GP*TP*AP*T)-3'), DNA (5'-D(*AP*CP*TP*GP*CP*TP*GP*AP*GP*TP*AP*CP*CP*AP*T)-3'), ... (5 entities in total)
• 機能のキーワード: sra, set, histone methylation, methylated dna, methylation, transcription-dna complex, transcription/dna
• 由来する生物種: Arabidopsis thaliana (mouse-ear cress,thale-cress)
• 細胞内の位置: Nucleus: Q8GZB6
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 69524.87

構造登録者

Du, J.,Li, S.,Patel, D.J. (登録日: 2014-05-17, 公開日: 2014-07-30, 最終更新日: 2023-09-20)

主引用文献

Du, J.,Johnson, L.M.,Groth, M.,Feng, S.,Hale, C.J.,Li, S.,Vashisht, A.A.,Gallego-Bartolome, J.,Wohlschlegel, J.A.,Patel, D.J.,Jacobsen, S.E.
Mechanism of DNA Methylation-Directed Histone Methylation by KRYPTONITE.
Mol.Cell, 55:495-504, 2014

PubMed Abstract: In Arabidopsis, CHG DNA methylation is controlled by the H3K9 methylation mark through a self-reinforcing loop between DNA methyltransferase CHROMOMETHYLASE3 (CMT3) and H3K9 histone methyltransferase KRYPTONITE/SUVH4 (KYP). We report on the structure of KYP in complex with methylated DNA, substrate H3 peptide, and cofactor SAH, thereby defining the spatial positioning of the SRA domain relative to the SET domain. The methylated DNA is bound by the SRA domain with the 5mC flipped out of the DNA, while the H3(1-15) peptide substrate binds between the SET and post-SET domains, with the ε-ammonium of K9 positioned adjacent to bound SAH. These structural insights, complemented by functional data on key mutants of residues lining the 5mC and H3K9-binding pockets within KYP, establish how methylated DNA recruits KYP to the histone substrate. Together, the structures of KYP and previously reported CMT3 complexes provide insights into molecular mechanisms linking DNA and histone methylation.

PubMed: 25018018
DOI: 10.1016/j.molcel.2014.06.009

実験手法

X-RAY DIFFRACTION (3.1 Å)