7vrr

Crystal structure of Arabidopsis thaliana HDT1Crystal structure of Arabidopsis thaliana HDT1

Structural highlights

7vrr is a 5 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.95Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HDT1_ARATH Probably mediates the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Required for histone H3 'Lys-9' deacetylation. Involved in rRNA gene silencing in nucleolar dominance. Seems to be implicated in the regulation of genes involved in seeds development.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

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.

Plant-specific HDT family histone deacetylases are nucleoplasmins.,Bobde RC, Kumar A, Vasudevan D Plant Cell. 2022 Sep 7. pii: 6693634. doi: 10.1093/plcell/koac275. PMID:36069647^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Wu K, Tian L, Malik K, Brown D, Miki B. Functional analysis of HD2 histone deacetylase homologues in Arabidopsis thaliana. Plant J. 2000 Apr;22(1):19-27. doi: 10.1046/j.1365-313x.2000.00711.x. PMID:10792817 doi:http://dx.doi.org/10.1046/j.1365-313x.2000.00711.x
↑ Wu K, Tian L, Zhou C, Brown D, Miki B. Repression of gene expression by Arabidopsis HD2 histone deacetylases. Plant J. 2003 Apr;34(2):241-7. PMID:12694598
↑ Lawrence RJ, Earley K, Pontes O, Silva M, Chen ZJ, Neves N, Viegas W, Pikaard CS. A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance. Mol Cell. 2004 Feb 27;13(4):599-609. doi: 10.1016/s1097-2765(04)00064-4. PMID:14992728 doi:http://dx.doi.org/10.1016/s1097-2765(04)00064-4
↑ Zhou C, Labbe H, Sridha S, Wang L, Tian L, Latoszek-Green M, Yang Z, Brown D, Miki B, Wu K. Expression and function of HD2-type histone deacetylases in Arabidopsis development. Plant J. 2004 Jun;38(5):715-24. PMID:15144374 doi:http://dx.doi.org/10.1111/j.1365-313X.2004.02083.x
↑ Bobde RC, Kumar A, Vasudevan D. Plant-specific HDT family histone deacetylases are nucleoplasmins. Plant Cell. 2022 Sep 7. pii: 6693634. doi: 10.1093/plcell/koac275. PMID:36069647 doi:http://dx.doi.org/10.1093/plcell/koac275

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OCA

[1] Wu K, Tian L, Malik K, Brown D, Miki B. Functional analysis of HD2 histone deacetylase homologues in Arabidopsis thaliana. Plant J. 2000 Apr;22(1):19-27. doi: 10.1046/j.1365-313x.2000.00711.x. PMID:10792817 doi:http://dx.doi.org/10.1046/j.1365-313x.2000.00711.x

[2] Wu K, Tian L, Zhou C, Brown D, Miki B. Repression of gene expression by Arabidopsis HD2 histone deacetylases. Plant J. 2003 Apr;34(2):241-7. PMID:12694598

[3] Lawrence RJ, Earley K, Pontes O, Silva M, Chen ZJ, Neves N, Viegas W, Pikaard CS. A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance. Mol Cell. 2004 Feb 27;13(4):599-609. doi: 10.1016/s1097-2765(04)00064-4. PMID:14992728 doi:http://dx.doi.org/10.1016/s1097-2765(04)00064-4

[4] Zhou C, Labbe H, Sridha S, Wang L, Tian L, Latoszek-Green M, Yang Z, Brown D, Miki B, Wu K. Expression and function of HD2-type histone deacetylases in Arabidopsis development. Plant J. 2004 Jun;38(5):715-24. PMID:15144374 doi:http://dx.doi.org/10.1111/j.1365-313X.2004.02083.x

[5] Bobde RC, Kumar A, Vasudevan D. Plant-specific HDT family histone deacetylases are nucleoplasmins. Plant Cell. 2022 Sep 7. pii: 6693634. doi: 10.1093/plcell/koac275. PMID:36069647 doi:http://dx.doi.org/10.1093/plcell/koac275

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