5ikk

From Proteopedia

(Difference between revisions)

Current revision

Structure of the histone deacetylase Clr3

Structural highlights

5ikk is a 1 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 2.4Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CLR3_SCHPO 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. Histone deacetylases act via the formation of large multiprotein complexes. 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]

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^[2]

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

References

↑ 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:http://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:http://dx.doi.org/10.1016/j.molcel.2016.03.016

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5ikk"

Categories: Large Structures | Schizosaccharomyces pombe 972h- | Brugger C | Schalch T

@@ Line 1: / Line 1: @@
 ==Structure of the histone deacetylase Clr3==
-<StructureSection load='5ikk' size='340' side='right' caption='[[5ikk]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='5ikk' size='340' side='right'caption='[[5ikk]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ikk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IKK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IKK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ikk]] is a 1 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=5IKK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IKK FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.4&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_deacetylase Histone deacetylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.98 3.5.1.98] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5ikk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ikk OCA], [http://pdbe.org/5ikk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ikk RCSB], [http://www.ebi.ac.uk/pdbsum/5ikk PDBsum]</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=5ikk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ikk OCA], [https://pdbe.org/5ikk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ikk RCSB], [https://www.ebi.ac.uk/pdbsum/5ikk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ikk ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CLR3_SCHPO CLR3_SCHPO]] 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. Histone deacetylases act via the formation of large multiprotein complexes. 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:17289569</ref>
+[https://www.uniprot.org/uniprot/CLR3_SCHPO CLR3_SCHPO] 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. Histone deacetylases act via the formation of large multiprotein complexes. 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:17289569</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 5ikk" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Histone deacetylase 3D structures|Histone deacetylase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Histone deacetylase]]
+[[Category: Large Structures]]
-[[Category: Brugger, C]]
+[[Category: Schizosaccharomyces pombe 972h-]]
-[[Category: Schalch, T]]
+[[Category: Brugger C]]
-[[Category: Alpha/beta hydrolase domain]]
+[[Category: Schalch T]]
-[[Category: Alpha/beta sandwich]]
-[[Category: Dimer]]
-[[Category: Hdac domain]]
-[[Category: Hydrolase]]
-[[Category: Transcription]]

5ikk

From Proteopedia

Current revision

Structure of the histone deacetylase Clr3

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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