6J6T

Crystal Structure of HDA15 HD domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of Arabidopsis HISTONE DEACETYLASE15.

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.

(2020) Plant Physiol 184: 1585-1600

  • DOI: https://doi.org/10.1104/pp.20.00604
  • Primary Citation of Related Structures:  
    6J6T

  • 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 ( Arabidopsis thaliana ). 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.


  • Organizational Affiliation

    Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase 15
A, B, C, D
364Arabidopsis thalianaMutation(s): 0 
Gene Names: HDA15At3g18520MYF24_23
EC: 3.5.1.98
UniProt
Find proteins for Q8GXJ1 (Arabidopsis thaliana)
Explore Q8GXJ1 
Go to UniProtKB:  Q8GXJ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GXJ1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
K [auth B]
L [auth B]
M [auth B]
G [auth A],
H [auth A],
K [auth B],
L [auth B],
M [auth B],
P [auth C],
S [auth D],
T [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
N [auth C],
Q [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
O [auth C],
R [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.809α = 90
b = 78.833β = 94.221
c = 176.794γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (Taiwan)Taiwan107-2313-B-002-003
Ministry of Science and Technology (Taiwan)Taiwan107-2311-B-002-010

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2020-11-18
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description