5ikj: Difference between revisions

Latest revision as of 13:58, 30 August 2023

Structure of Clr2 bound to the Clr1 C-terminus

Structural highlights

5ikj is a 2 chain structure with sequence from Schizosaccharomyces pombe 972h-. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Ligands:	CL, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CLR2_SCHPO Required for deacetylation in the mating-type region and the centromere. Acts upstream of the histone deacetylases to promote transcriptional silencing. Required for proper positioning of nucleosomes at heterochromatic loci and for transcriptional gene silencing (TGS) function of the Snf2/Hdac-containing repressor complex (SHREC).^[1] ^[2]

Publication Abstract from PubMed

Nucleosome remodeling and deacetylation (NuRD) complexes are co-transcriptional regulators implicated in differentiation, development, and diseases. Methyl-CpG binding domain (MBD) proteins play an essential role in recruitment of NuRD complexes to their target sites in chromatin. The related SHREC complex in fission yeast drives transcriptional gene silencing in heterochromatin through cooperation with HP1 proteins. How remodeler and histone deacetylase (HDAC) cooperate within NuRD complexes remains unresolved. We determined that in SHREC the two modules occupy distant sites on the scaffold protein Clr1 and that repressive activity of SHREC can be modulated by the expression level of the HDAC-associated Clr1 domain alone. Moreover, the crystal structure of Clr2 reveals an MBD-like domain mediating recruitment of the HDAC module to heterochromatin. Thus, SHREC bi-functionality is organized in two separate modules with separate recruitment mechanisms, which work together to elicit transcriptional silencing at heterochromatic loci.

SHREC Silences Heterochromatin via Distinct Remodeling and Deacetylation Modules.,Job G, Brugger C, Xu T, Lowe BR, Pfister Y, Qu C, Shanker S, Banos Sanz JI, Partridge JF, Schalch T Mol Cell. 2016 Apr 21;62(2):207-21. doi: 10.1016/j.molcel.2016.03.016. PMID:27105116^[3]

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

References

↑ Bjerling P, Ekwall K, Egel R, Thon G. A novel type of silencing factor, Clr2, is necessary for transcriptional silencing at various chromosomal locations in the fission yeast Schizosaccharomyces pombe. Nucleic Acids Res. 2004 Aug 18;32(15):4421-8. Print 2004. PMID:15317867 doi:https://dx.doi.org/10.1093/nar/gkh780
↑ Sugiyama T, Cam HP, Sugiyama R, Noma K, Zofall M, Kobayashi R, Grewal SI. SHREC, an effector complex for heterochromatic transcriptional silencing. Cell. 2007 Feb 9;128(3):491-504. PMID:17289569 doi:https://dx.doi.org/10.1016/j.cell.2006.12.035
↑ Job G, Brugger C, Xu T, Lowe BR, Pfister Y, Qu C, Shanker S, Banos Sanz JI, Partridge JF, Schalch T. SHREC Silences Heterochromatin via Distinct Remodeling and Deacetylation Modules. Mol Cell. 2016 Apr 21;62(2):207-21. doi: 10.1016/j.molcel.2016.03.016. PMID:27105116 doi:https://dx.doi.org/10.1016/j.molcel.2016.03.016

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OCA

[1] Bjerling P, Ekwall K, Egel R, Thon G. A novel type of silencing factor, Clr2, is necessary for transcriptional silencing at various chromosomal locations in the fission yeast Schizosaccharomyces pombe. Nucleic Acids Res. 2004 Aug 18;32(15):4421-8. Print 2004. PMID:15317867 doi:https://dx.doi.org/10.1093/nar/gkh780

[2] Sugiyama T, Cam HP, Sugiyama R, Noma K, Zofall M, Kobayashi R, Grewal SI. SHREC, an effector complex for heterochromatic transcriptional silencing. Cell. 2007 Feb 9;128(3):491-504. PMID:17289569 doi:https://dx.doi.org/10.1016/j.cell.2006.12.035

[3] Job G, Brugger C, Xu T, Lowe BR, Pfister Y, Qu C, Shanker S, Banos Sanz JI, Partridge JF, Schalch T. SHREC Silences Heterochromatin via Distinct Remodeling and Deacetylation Modules. Mol Cell. 2016 Apr 21;62(2):207-21. doi: 10.1016/j.molcel.2016.03.016. PMID:27105116 doi:https://dx.doi.org/10.1016/j.molcel.2016.03.016

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==Structure of Clr2 bound to the Clr1 C-terminus==
-<StructureSection load='5ikj' size='340' side='right' caption='[[5ikj]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='5ikj' size='340' side='right'caption='[[5ikj]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ikj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Fission_yeast Fission yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IKJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IKJ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ikj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe_972h- Schizosaccharomyces pombe 972h-]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IKJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IKJ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">clr2, SPAC1B3.17 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast]), clr1, SPBC2D10.17 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ikj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ikj OCA], [http://pdbe.org/5ikj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ikj RCSB], [http://www.ebi.ac.uk/pdbsum/5ikj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ikj ProSAT]</span></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=5ikj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ikj OCA], [https://pdbe.org/5ikj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ikj RCSB], [https://www.ebi.ac.uk/pdbsum/5ikj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ikj ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CLR2_SCHPO CLR2_SCHPO]] Required for deacetylation in the mating-type region and the centromere. Acts upstream of the histone deacetylases to promote transcriptional silencing. Required for proper positioning of nucleosomes at heterochromatic loci and for transcriptional gene silencing (TGS) function of the Snf2/Hdac-containing repressor complex (SHREC).<ref>PMID:15317867</ref> <ref>PMID:17289569</ref>  [[http://www.uniprot.org/uniprot/CLR1_SCHPO CLR1_SCHPO]] Regulates silencing of the mat2 and mat3 loci. Organizes the chromatin structure of the mating-type region where it also participates in establishing the 'cold spot' for recombination. Required for proper positioning of nucleosomes at heterochromatic loci and for transcriptional gene silencing (TGS) function of the Snf2/Hdac-containing repressor complex (SHREC).<ref>PMID:1644273</ref> <ref>PMID:17289569</ref>
+[https://www.uniprot.org/uniprot/CLR2_SCHPO CLR2_SCHPO] Required for deacetylation in the mating-type region and the centromere. Acts upstream of the histone deacetylases to promote transcriptional silencing. Required for proper positioning of nucleosomes at heterochromatic loci and for transcriptional gene silencing (TGS) function of the Snf2/Hdac-containing repressor complex (SHREC).<ref>PMID:15317867</ref> <ref>PMID:17289569</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Fission yeast]]
+[[Category: Large Structures]]
-[[Category: Pfister, Y]]
+[[Category: Schizosaccharomyces pombe 972h-]]
-[[Category: Schalch, T]]
+[[Category: Pfister Y]]
-[[Category: Bah domain]]
+[[Category: Schalch T]]
-[[Category: Cell cycle]]
-[[Category: Chromobarrel domain]]
-[[Category: Complex]]
-[[Category: Methyl-cpg-binding domain]]
-[[Category: Transcription]]

5ikj: Difference between revisions

Latest revision as of 13:58, 30 August 2023

Structure of Clr2 bound to the Clr1 C-terminus

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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