In this study, a comparative analysis of the amino acid sequences and domain organization of histone deacetylases (HDACs) from Arabidopsis thaliana and Oryza sativa was performed, and the presence of experimentally determined 3D structures as well as the quality of predicted models was assessed. The results of the analysis of deacetylase inhibitor binding across different classes demonstrated their limited selectivity toward plant HDACs. Notable inhibitory selectivity was observed for SAHA, whereas trichostatin A, sodium butyrate, and cyclic hydroxamic acid derivatives acted predominantly as pan-HDACis (HDAC inhibitors). It was shown that sodium butyrate can bind within the catalytic pocket of deacetylases; however, its interaction is unstable and likely induces inhibition by triggering conformational changes. The structural analysis provided a detailed characterization of the shared and distinct features of the HDACs examined. HDAC10 from O. sativa was found to exhibit the highest structural similarity to HDA14 from A. thaliana, suggesting a potentially similar functional role and shared deacetylation substrates. Four key amino acid residues required for Zn2+ coordination in the active site were identified, including the “XDXH” motif, which is critically important for catalytic activity. The results obtained enhance our understanding of the structural organization of plant HDACs, identify key determinants of their catalytic activity, and provide a foundation for the development of selective inhibitors and biotechnological strategies aimed at regulating plant growth and improving stress tolerance.
Stykhylias et al. (Mon,) studied this question.