7yi4: Difference between revisions

Revision as of 11:09, 2 August 2023

Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in close state

Structural highlights

7yi4 is a 16 chain structure with sequence from Saccharomyces cerevisiae S288C, 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 3.96Å
Ligands:	M3L, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SIN3_YEAST Catalytic component of the RPD3 histone deacetylase 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 gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. SIN3 has also a RPD3 independent function required for normal longevity.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13] ^[14] ^[15] ^[16] ^[17] ^[18]

References

↑ 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
↑ Washburn BK, Esposito RE. Identification of the Sin3-binding site in Ume6 defines a two-step process for conversion of Ume6 from a transcriptional repressor to an activator in yeast. Mol Cell Biol. 2001 Mar;21(6):2057-69. PMID:11238941 doi:10.1128/MCB.21.6.2057-2069.2001
↑ 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
↑ Kaeberlein M, Kirkland KT, Fields S, Kennedy BK. Genes determining yeast replicative life span in a long-lived genetic background. Mech Ageing Dev. 2005 Apr;126(4):491-504. PMID:15722108 doi:10.1016/j.mad.2004.10.007
↑ Yoshimoto H, Ohmae M, Yamashita I. The Saccharomyces cerevisiae GAM2/SIN3 protein plays a role in both activation and repression of transcription. Mol Gen Genet. 1992 May;233(1-2):327-30. PMID:1603074 doi:10.1007/BF00587597
↑ 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, Strich R, Esposito RE, Gaber RF. RPD1 (SIN3/UME4) is required for maximal activation and repression of diverse yeast genes. Mol Cell Biol. 1991 Dec;11(12):6306-16. PMID:1944290 doi:10.1128/mcb.11.12.6306-6316.1991
↑ Wang H, Clark I, Nicholson PR, Herskowitz I, Stillman DJ. The Saccharomyces cerevisiae SIN3 gene, a negative regulator of HO, contains four paired amphipathic helix motifs. Mol Cell Biol. 1990 Nov;10(11):5927-36. PMID:2233725 doi:10.1128/mcb.10.11.5927-5936.1990
↑ Wang H, Stillman DJ. Transcriptional repression in Saccharomyces cerevisiae by a SIN3-LexA fusion protein. Mol Cell Biol. 1993 Mar;13(3):1805-14. PMID:8441414 doi:10.1128/mcb.13.3.1805-1814.1993
↑ 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
↑ Kasten MM, Dorland S, Stillman DJ. A large protein complex containing the yeast Sin3p and Rpd3p transcriptional regulators. Mol Cell Biol. 1997 Aug;17(8):4852-8. PMID:9234741 doi:10.1128/MCB.17.8.4852
↑ Rundlett SE, Carmen AA, Suka N, Turner BM, Grunstein M. Transcriptional repression by UME6 involves deacetylation of lysine 5 of histone H4 by RPD3. Nature. 1998 Apr 23;392(6678):831-5. PMID:9572144 doi:10.1038/33952
↑ 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

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OCA

[1] 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

[2] 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

[3] Washburn BK, Esposito RE. Identification of the Sin3-binding site in Ume6 defines a two-step process for conversion of Ume6 from a transcriptional repressor to an activator in yeast. Mol Cell Biol. 2001 Mar;21(6):2057-69. PMID:11238941 doi:10.1128/MCB.21.6.2057-2069.2001

[4] 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

[5] 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

[6] 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

[7] 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

[8] 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

[9] Kaeberlein M, Kirkland KT, Fields S, Kennedy BK. Genes determining yeast replicative life span in a long-lived genetic background. Mech Ageing Dev. 2005 Apr;126(4):491-504. PMID:15722108 doi:10.1016/j.mad.2004.10.007

[10] Yoshimoto H, Ohmae M, Yamashita I. The Saccharomyces cerevisiae GAM2/SIN3 protein plays a role in both activation and repression of transcription. Mol Gen Genet. 1992 May;233(1-2):327-30. PMID:1603074 doi:10.1007/BF00587597

[11] 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

[12] Vidal M, Strich R, Esposito RE, Gaber RF. RPD1 (SIN3/UME4) is required for maximal activation and repression of diverse yeast genes. Mol Cell Biol. 1991 Dec;11(12):6306-16. PMID:1944290 doi:10.1128/mcb.11.12.6306-6316.1991

[13] Wang H, Clark I, Nicholson PR, Herskowitz I, Stillman DJ. The Saccharomyces cerevisiae SIN3 gene, a negative regulator of HO, contains four paired amphipathic helix motifs. Mol Cell Biol. 1990 Nov;10(11):5927-36. PMID:2233725 doi:10.1128/mcb.10.11.5927-5936.1990

[14] Wang H, Stillman DJ. Transcriptional repression in Saccharomyces cerevisiae by a SIN3-LexA fusion protein. Mol Cell Biol. 1993 Mar;13(3):1805-14. PMID:8441414 doi:10.1128/mcb.13.3.1805-1814.1993

[15] 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

[16] Kasten MM, Dorland S, Stillman DJ. A large protein complex containing the yeast Sin3p and Rpd3p transcriptional regulators. Mol Cell Biol. 1997 Aug;17(8):4852-8. PMID:9234741 doi:10.1128/MCB.17.8.4852

[17] Rundlett SE, Carmen AA, Suka N, Turner BM, Grunstein M. Transcriptional repression by UME6 involves deacetylation of lysine 5 of histone H4 by RPD3. Nature. 1998 Apr 23;392(6678):831-5. PMID:9572144 doi:10.1038/33952

[18] 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

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 == Structural highlights ==
 <table><tr><td colspan='2'>[[7yi4]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C], [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=7YI4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YI4 FirstGlance]. <br>
-</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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.96&#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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7yi4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yi4 OCA], [https://pdbe.org/7yi4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yi4 RCSB], [https://www.ebi.ac.uk/pdbsum/7yi4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yi4 ProSAT]</span></td></tr>
 </table>

7yi4: Difference between revisions

Revision as of 11:09, 2 August 2023

Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in close state

Structural highlights

Function

References

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