5y26: Difference between revisions

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==Crystal structure of native Dpb4-Dpb3==
==Crystal structure of native Dpb4-Dpb3==
<StructureSection load='5y26' size='340' side='right' caption='[[5y26]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='5y26' size='340' side='right'caption='[[5y26]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5y26]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y26 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y26 FirstGlance]. <br>
<table><tr><td colspan='2'>[[5y26]] 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=5Y26 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y26 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.003&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=5y26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y26 OCA], [http://pdbe.org/5y26 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y26 RCSB], [http://www.ebi.ac.uk/pdbsum/5y26 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y26 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=5y26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y26 OCA], [https://pdbe.org/5y26 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y26 RCSB], [https://www.ebi.ac.uk/pdbsum/5y26 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y26 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/DPB4_SCHPO DPB4_SCHPO]] DNA polymerase II participates in chromosomal DNA replication. Not essential for cell cycle progression.<ref>PMID:15388803</ref> [[http://www.uniprot.org/uniprot/YCGV_SCHPO YCGV_SCHPO]] Putative transcription factor.
[https://www.uniprot.org/uniprot/DPB4_SCHPO DPB4_SCHPO] DNA polymerase II participates in chromosomal DNA replication. Not essential for cell cycle progression.<ref>PMID:15388803</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
During DNA replication, chromatin is disrupted ahead of the replication fork, and epigenetic information must be restored behind the fork. How epigenetic marks are inherited through DNA replication remains poorly understood. Histone H3 lysine 9 (H3K9) methylation and histone hypoacetylation are conserved hallmarks of heterochromatin. We previously showed that the inheritance of H3K9 methylation during DNA replication depends on the catalytic subunit of DNA polymerase epsilon, Cdc20. Here we show that the histone-fold subunit of Pol epsilon, Dpb4, interacts an uncharacterized small histone-fold protein, SPCC16C4.22, to form a heterodimer in fission yeast. We demonstrate that SPCC16C4.22 is nonessential for viability and corresponds to the true ortholog of Dpb3. We further show that the Dpb3-Dpb4 dimer associates with histone deacetylases, chromatin remodelers, and histones and plays a crucial role in the inheritance of histone hypoacetylation in heterochromatin. We solve the 1.9-A crystal structure of Dpb3-Dpb4 and reveal that they form the H2A-H2B-like dimer. Disruption of Dpb3-Dpb4 dimerization results in loss of heterochromatin silencing. Our findings reveal a link between histone deacetylation and H3K9 methylation and suggest a mechanism for how two processes are coordinated during replication. We propose that the Dpb3-Dpb4 heterodimer together with Cdc20 serves as a platform for the recruitment of chromatin modifiers and remodelers that mediate heterochromatin assembly during DNA replication, and ensure the faithful inheritance of epigenetic marks in heterochromatin.


Coordinated regulation of heterochromatin inheritance by Dpb3-Dpb4 complex.,He H, Li Y, Dong Q, Chang AY, Gao F, Chi Z, Su M, Zhang F, Ban H, Martienssen R, Chen YH, Li F Proc Natl Acad Sci U S A. 2017 Nov 21;114(47):12524-12529. doi:, 10.1073/pnas.1712961114. Epub 2017 Nov 6. PMID:29109278<ref>PMID:29109278</ref>
==See Also==
 
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5y26" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: DNA-directed DNA polymerase]]
[[Category: Large Structures]]
[[Category: Chen, Y H]]
[[Category: Schizosaccharomyces pombe 972h-]]
[[Category: Gao, F]]
[[Category: Chen YH]]
[[Category: Li, Y]]
[[Category: Gao F]]
[[Category: Dna binding]]
[[Category: Li Y]]
[[Category: Dna binding protein]]
[[Category: Epigenetic]]
[[Category: Heterodimer]]
[[Category: Histone fold complex]]

Latest revision as of 13:21, 27 March 2024

Crystal structure of native Dpb4-Dpb3Crystal structure of native Dpb4-Dpb3

Structural highlights

5y26 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 2.003Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DPB4_SCHPO DNA polymerase II participates in chromosomal DNA replication. Not essential for cell cycle progression.[1]

See Also

References

  1. ↑ Spiga MG, D'Urso G. Identification and cloning of two putative subunits of DNA polymerase epsilon in fission yeast. Nucleic Acids Res. 2004 Sep 23;32(16):4945-53. doi: 10.1093/nar/gkh811. Print, 2004. PMID:15388803 doi:http://dx.doi.org/10.1093/nar/gkh811

5y26, resolution 2.00Å

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