8kd7

From Proteopedia

(Difference between revisions)

Revision as of 18:18, 20 September 2023

Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA

Structural highlights

8kd7 is a 16 chain structure with sequence from Saccharomyces cerevisiae, Xenopus laevis and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.09Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RPD3_YEAST Catalytic component of the RPD3 histone deacetylase (HDAC) complexes RPD3C(L) and RPD3C(S) responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation plays an important role in transcriptional regulation, cell cycle progression, DNA damage response, osmotic stress response and developmental events. Is involved in rDNA and telomere silencing and in double strand breaks repair. Required for both full transcription repression and activation of many genes including cell type-specific genes (STE6, TY2 and HO), cell differentiation-specific genes (SPO13), genes that respond to external signals (PHO5) and TRK2. The RPD3 complexes regulate also chromosomal replication timing.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13] ^[14] ^[15] ^[16] ^[17] ^[18] ^[19]

Publication Abstract from PubMed

In Saccharomyces cerevisiae, cryptic transcription at the coding region is prevented by the activity of Sin3 histone deacetylase (HDAC) complex Rpd3S, which is carried by the transcribing RNA polymerase II (RNAPII) to deacetylate and stabilize chromatin. Despite its fundamental importance, the mechanisms by which Rpd3S deacetylates nucleosomes and regulates chromatin dynamics remain elusive. Here, we determined several cryo-EM structures of Rpd3S in complex with nucleosome core particles (NCPs), including the H3/H4 deacetylation states, the alternative deacetylation state, the linker tightening state, and a state in which Rpd3S co-exists with the Hho1 linker histone on NCP. These structures suggest that Rpd3S utilizes a conserved Sin3 basic surface to navigate through the nucleosomal DNA, guided by its interactions with H3K36 methylation and the extra-nucleosomal DNA linkers, to target acetylated H3K9 and sample other histone tails. Furthermore, our structures illustrate that Rpd3S reconfigures the DNA linkers and acts in concert with Hho1 to engage the NCP, potentially unraveling how Rpd3S and Hho1 work in tandem for gene silencing.

Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex.,Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J Cell Res. 2023 Sep 4. doi: 10.1038/s41422-023-00869-1. PMID:37666978^[20]

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

References

↑ Dora EG, Rudin N, Martell JR, Esposito MS, Ramírez RM. RPD3 (REC3) mutations affect mitotic recombination in Saccharomyces cerevisiae. Curr Genet. 1999 Mar;35(2):68-76. PMID:10079324 doi:10.1007/s002940050434
↑ Burgess SM, Ajimura M, Kleckner N. GCN5-dependent histone H3 acetylation and RPD3-dependent histone H4 deacetylation have distinct, opposing effects on IME2 transcription, during meiosis and during vegetative growth, in budding yeast. Proc Natl Acad Sci U S A. 1999 Jun 8;96(12):6835-40. PMID:10359799 doi:10.1073/pnas.96.12.6835
↑ Sun ZW, Hampsey M. A general requirement for the Sin3-Rpd3 histone deacetylase complex in regulating silencing in Saccharomyces cerevisiae. Genetics. 1999 Jul;152(3):921-32. PMID:10388812 doi:10.1093/genetics/152.3.921
↑ Elkhaimi M, Kaadige MR, Kamath D, Jackson JC, Biliran H Jr, Lopes JM. Combinatorial regulation of phospholipid biosynthetic gene expression by the UME6, SIN3 and RPD3 genes. Nucleic Acids Res. 2000 Aug 15;28(16):3160-7. PMID:10931932 doi:10.1093/nar/28.16.3160
↑ Watson AD, Edmondson DG, Bone JR, Mukai Y, Yu Y, Du W, Stillman DJ, Roth SY. Ssn6-Tup1 interacts with class I histone deacetylases required for repression. Genes Dev. 2000 Nov 1;14(21):2737-44. PMID:11069890
↑ Kurdistani SK, Robyr D, Tavazoie S, Grunstein M. Genome-wide binding map of the histone deacetylase Rpd3 in yeast. Nat Genet. 2002 Jul;31(3):248-54. PMID:12089521 doi:10.1038/ng907
↑ Deckert J, Struhl K. Targeted recruitment of Rpd3 histone deacetylase represses transcription by inhibiting recruitment of Swi/Snf, SAGA, and TATA binding protein. Mol Cell Biol. 2002 Sep;22(18):6458-70. PMID:12192044 doi:10.1128/MCB.22.18.6458-6470.2002
↑ Scott KL, Plon SE. Loss of Sin3/Rpd3 histone deacetylase restores the DNA damage response in checkpoint-deficient strains of Saccharomyces cerevisiae. Mol Cell Biol. 2003 Jul;23(13):4522-31. PMID:12808094 doi:10.1128/MCB.23.13.4522-4531.2003
↑ Jazayeri A, McAinsh AD, Jackson SP. Saccharomyces cerevisiae Sin3p facilitates DNA double-strand break repair. Proc Natl Acad Sci U S A. 2004 Feb 10;101(6):1644-9. PMID:14711989 doi:10.1073/pnas.0304797101
↑ De Nadal E, Zapater M, Alepuz PM, Sumoy L, Mas G, Posas F. The MAPK Hog1 recruits Rpd3 histone deacetylase to activate osmoresponsive genes. Nature. 2004 Jan 22;427(6972):370-4. PMID:14737171 doi:10.1038/nature02258
↑ Schröder M, Clark R, Liu CY, Kaufman RJ. The unfolded protein response represses differentiation through the RPD3-SIN3 histone deacetylase. EMBO J. 2004 Jun 2;23(11):2281-92. PMID:15141165 doi:10.1038/sj.emboj.7600233
↑ Aparicio JG, Viggiani CJ, Gibson DG, Aparicio OM. The Rpd3-Sin3 histone deacetylase regulates replication timing and enables intra-S origin control in Saccharomyces cerevisiae. Mol Cell Biol. 2004 Jun;24(11):4769-80. PMID:15143171 doi:10.1128/MCB.24.11.4769-4780.2004
↑ Sabet N, Volo S, Yu C, Madigan JP, Morse RH. Genome-wide analysis of the relationship between transcriptional regulation by Rpd3p and the histone H3 and H4 amino termini in budding yeast. Mol Cell Biol. 2004 Oct;24(20):8823-33. PMID:15456858 doi:10.1128/MCB.24.20.8823-8833.2004
↑ Keogh MC, Kurdistani SK, Morris SA, Ahn SH, Podolny V, Collins SR, Schuldiner M, Chin K, Punna T, Thompson NJ, Boone C, Emili A, Weissman JS, Hughes TR, Strahl BD, Grunstein M, Greenblatt JF, Buratowski S, Krogan NJ. Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell. 2005 Nov 18;123(4):593-605. PMID:16286008 doi:10.1016/j.cell.2005.10.025
↑ Vidal M, Gaber RF. RPD3 encodes a second factor required to achieve maximum positive and negative transcriptional states in Saccharomyces cerevisiae. Mol Cell Biol. 1991 Dec;11(12):6317-27. PMID:1944291 doi:10.1128/mcb.11.12.6317-6327.1991
↑ Rundlett SE, Carmen AA, Kobayashi R, Bavykin S, Turner BM, Grunstein M. HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription. Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14503-8. PMID:8962081 doi:10.1073/pnas.93.25.14503
↑ Vannier D, Balderes D, Shore D. Evidence that the transcriptional regulators SIN3 and RPD3, and a novel gene (SDS3) with similar functions, are involved in transcriptional silencing in S. cerevisiae. Genetics. 1996 Dec;144(4):1343-53. PMID:8978024 doi:10.1093/genetics/144.4.1343
↑ Kadosh D, Struhl K. Histone deacetylase activity of Rpd3 is important for transcriptional repression in vivo. Genes Dev. 1998 Mar 15;12(6):797-805. PMID:9512514 doi:10.1101/gad.12.6.797
↑ Kadosh D, Struhl K. Targeted recruitment of the Sin3-Rpd3 histone deacetylase complex generates a highly localized domain of repressed chromatin in vivo. Mol Cell Biol. 1998 Sep;18(9):5121-7. PMID:9710596 doi:10.1128/MCB.18.9.5121
↑ Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J. Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex. Cell Res. 2023 Sep 4. PMID:37666978 doi:10.1038/s41422-023-00869-1

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/8kd7"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8kd7 is ON HOLD  until Paper Publication
+==Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA==
+<StructureSection load='8kd7' size='340' side='right'caption='[[8kd7]], [[Resolution|resolution]] 3.09&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8kd7]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae], [https://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8KD7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8KD7 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.09&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8kd7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8kd7 OCA], [https://pdbe.org/8kd7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8kd7 RCSB], [https://www.ebi.ac.uk/pdbsum/8kd7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8kd7 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RPD3_YEAST RPD3_YEAST] Catalytic component of the RPD3 histone deacetylase (HDAC) complexes RPD3C(L) and RPD3C(S) responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation plays an important role in transcriptional regulation, cell cycle progression, DNA damage response, osmotic stress response and developmental events. Is involved in rDNA and telomere silencing and in double strand breaks repair. Required for both full transcription repression and activation of many genes including cell type-specific genes (STE6, TY2 and HO), cell differentiation-specific genes (SPO13), genes that respond to external signals (PHO5) and TRK2. The RPD3 complexes regulate also chromosomal replication timing.<ref>PMID:10079324</ref> <ref>PMID:10359799</ref> <ref>PMID:10388812</ref> <ref>PMID:10931932</ref> <ref>PMID:11069890</ref> <ref>PMID:12089521</ref> <ref>PMID:12192044</ref> <ref>PMID:12808094</ref> <ref>PMID:14711989</ref> <ref>PMID:14737171</ref> <ref>PMID:15141165</ref> <ref>PMID:15143171</ref> <ref>PMID:15456858</ref> <ref>PMID:16286008</ref> <ref>PMID:1944291</ref> <ref>PMID:8962081</ref> <ref>PMID:8978024</ref> <ref>PMID:9512514</ref> <ref>PMID:9710596</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In Saccharomyces cerevisiae, cryptic transcription at the coding region is prevented by the activity of Sin3 histone deacetylase (HDAC) complex Rpd3S, which is carried by the transcribing RNA polymerase II (RNAPII) to deacetylate and stabilize chromatin. Despite its fundamental importance, the mechanisms by which Rpd3S deacetylates nucleosomes and regulates chromatin dynamics remain elusive. Here, we determined several cryo-EM structures of Rpd3S in complex with nucleosome core particles (NCPs), including the H3/H4 deacetylation states, the alternative deacetylation state, the linker tightening state, and a state in which Rpd3S co-exists with the Hho1 linker histone on NCP. These structures suggest that Rpd3S utilizes a conserved Sin3 basic surface to navigate through the nucleosomal DNA, guided by its interactions with H3K36 methylation and the extra-nucleosomal DNA linkers, to target acetylated H3K9 and sample other histone tails. Furthermore, our structures illustrate that Rpd3S reconfigures the DNA linkers and acts in concert with Hho1 to engage the NCP, potentially unraveling how Rpd3S and Hho1 work in tandem for gene silencing.
-Authors: Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Chang, X., Chao, W.C.H., He, J.
+Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex.,Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J Cell Res. 2023 Sep 4. doi: 10.1038/s41422-023-00869-1. PMID:37666978<ref>PMID:37666978</ref>
-Description: Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Wang, M]]
+<div class="pdbe-citations 8kd7" style="background-color:#fffaf0;"></div>
-[[Category: Li, H]]
+== References ==
-[[Category: Dong, S]]
+<references/>
-[[Category: Shi, X]]
+__TOC__
-[[Category: Chao, W.C.H]]
+</StructureSection>
-[[Category: Gao, X]]
+[[Category: Large Structures]]
-[[Category: Li, W]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Rasheed, N]]
+[[Category: Synthetic construct]]
-[[Category: Zhang, Y]]
+[[Category: Xenopus laevis]]
-[[Category: Guan, J]]
+[[Category: Chang X]]
-[[Category: Wang, C]]
+[[Category: Chao WCH]]
-[[Category: He, J]]
+[[Category: Dong S]]
-[[Category: Chang, X]]
+[[Category: Gao X]]
-[[Category: Huang, J]]
+[[Category: Guan J]]
-[[Category: Li, M]]
+[[Category: He J]]
-[[Category: Zhou, N]]
+[[Category: Huang J]]
-[[Category: Zhou, M]]
+[[Category: Li H]]
-[[Category: Zhang, J]]
+[[Category: Li M]]
-[[Category: Zou, B]]
+[[Category: Li W]]
-[[Category: Wong, K.H]]
+[[Category: Rasheed N]]
+[[Category: Shi X]]
+[[Category: Wang C]]
+[[Category: Wang M]]
+[[Category: Wong KH]]
+[[Category: Zhang J]]
+[[Category: Zhang Y]]
+[[Category: Zhou M]]
+[[Category: Zhou N]]
+[[Category: Zou B]]

8kd7

From Proteopedia

Revision as of 18:18, 20 September 2023

Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA

Structural highlights

Function

Publication Abstract from PubMed

References

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