7VMF

Crystal structure of Arabidopsis thaliana HDT2

7VMF の概要

• エントリーDOI: 10.2210/pdb7vmf/pdb
• 分子名称: Histone deacetylase HDT2, SODIUM ION (3 entities in total)
• 機能のキーワード: hdt, hd-tuin, nucleoplasmin, histone chaperone, hd2b, hdt2, chaperone
• 由来する生物種: Arabidopsis thaliana (Mouse-ear cress)
• タンパク質・核酸の鎖数: 5
• 化学式量合計: 51851.64

構造登録者

Kumar, A.,Bobde, R.C.,Vasudevan, D. (登録日: 2021-10-08, 公開日: 2022-09-21, 最終更新日: 2023-11-29)

主引用文献

Bobde, R.C.,Kumar, A.,Vasudevan, D.
Plant-specific HDT family histone deacetylases are nucleoplasmins.
Plant Cell, 34:4760-4777, 2022

PubMed Abstract: Histone acetyltransferase (HAT)- and histone deacetylase (HDAC)-mediated histone acetylation and deacetylation regulate nucleosome dynamics and gene expression. HDACs are classified into different families, with HD-tuins or HDTs being specific to plants. HDTs show some sequence similarity to nucleoplasmins, the histone chaperones that aid in binding, storing, and loading H2A/H2B dimers to assemble nucleosomes. Here, we solved the crystal structure of the N-terminal domain (NTD) of all four HDTs (HDT1, HDT2, HDT3, and HDT4) from Arabidopsis (Arabidopsis thaliana). The NTDs form a nucleoplasmin fold, exist as pentamers in solution, and are resistant to protease treatment, high temperature, salt, and urea conditions. Structurally, HDTs do not form a decamer, unlike certain classical nucleoplasmins. The HDT-NTD requires an additional A2 acidic tract C-terminal to the nucleoplasmin domain for interaction with histone H3/H4 and H2A/H2B oligomers. We also report the in-solution structures of HDT2 pentamers in complex with histone oligomers. Our study provides a detailed structural and in vitro functional characterization of HDTs, revealing them to be nucleoplasmin family histone chaperones. The experimental confirmation that HDTs are nucleoplasmins may spark new interest in this enigmatic family of proteins.

PubMed: 36069647
DOI: 10.1093/plcell/koac275

実験手法

X-RAY DIFFRACTION (1.32 Å)