6J6T

Crystal Structure of HDA15 HD domain

Summary for 6J6T

• Entry DOI: 10.2210/pdb6j6t/pdb
• Descriptor: Histone deacetylase 15, ZINC ION, POTASSIUM ION, ... (5 entities in total)
• Functional Keywords: histone deacetylase, arabidopsis, gene regulation
• Biological source: Arabidopsis thaliana (Mouse-ear cress)
• Total number of polymer chains: 4
• Total formula weight: 156677.88

Authors

Cheng, Y.S.,Hsu, J.C.,Hung, H.C.,Liu, T.C. (deposition date: 2019-01-15, release date: 2020-01-22, Last modification date: 2023-11-22)

Primary citation

Chen, C.Y.,Tu, Y.T.,Hsu, J.C.,Hung, H.C.,Liu, T.C.,Lee, Y.H.,Chou, C.C.,Cheng, Y.S.,Wu, K.
Structure of Arabidopsis HISTONE DEACETYLASE15.
Plant Physiol., 184:1585-1600, 2020

PubMed Abstract: Mammalian histone deacetylases (HDACs) undergo phosphorylation to regulate their localization, activity, and function. However, little is known about the regulation of plant HDAC function and activity by phosphorylation. Here, we report the crystal structure of the Reduced Potassium Dependency3/Histone Deacetylase1 (RPD3/HDA1) type class II histone deacetylase HDA15 in Arabidopsis (). The histone deacetylase domain of HDA15 (HDA15HD) assembles as tetrameric forms with each monomer composed of 12 α-helices and 9 β-sheets. The L1 loop and β2 sheet of HDA15HD are the essential interfaces for the tetramer formation. The N-terminal zinc finger domain enhances HDA15HD dimerization and increases its enzymatic activity. Furthermore, HDA15 can also be phosphorylated at Ser-448 and Ser-452 in etiolated seedlings. The HDA15 phosphorylation status determines its subnuclear localization and oligomerization. Phosphomimetics of HDA15 partially disrupt its oligomerization and cause loss of enzymatic activity and translocation from the nucleolus into nucleoplasm. Together, these data indicate that phosphorylation plays a critical role in regulating the structure and function of HDA15.

PubMed: 32878973
DOI: 10.1104/pp.20.00604

Experimental method

X-RAY DIFFRACTION (2.36 Å)