2yba

From Proteopedia

(Difference between revisions)

Revision as of 08:11, 23 August 2023

Crystal structure of Nurf55 in complex with histone H3

Structural highlights

2yba is a 4 chain structure with sequence from Drosophila melanogaster. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.55Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CAF1_DROME Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA. Component of several complexes which regulate chromatin metabolism. These include the chromatin assembly factor 1 (CAF-1) complex, which is required for chromatin assembly following DNA replication and DNA repair; the nucleosome remodeling and deacetylase complex (the NuRD complex), which promotes transcriptional repression by histone deacetylation and nucleosome remodeling; the nucleosome remodeling factor (NURF) complex, which catalyzes ATP-dependent nucleosome sliding and facilitates transcription of chromatin; and the polycomb group (PcG) repressor complex ESC-E(Z), which promotes repression of homeotic genes during development. Also required for transcriptional repression of E2F target genes by E2f2 and Rbf or Rbf2.^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

The Polycomb repressive complex 2 (PRC2) confers transcriptional repression through histone H3 lysine 27 trimethylation (H3K27me3). Here, we examined how PRC2 is modulated by histone modifications associated with transcriptionally active chromatin. We provide the molecular basis of histone H3 N terminus recognition by the PRC2 Nurf55-Su(z)12 submodule. Binding of H3 is lost if lysine 4 in H3 is trimethylated. We find that H3K4me3 inhibits PRC2 activity in an allosteric fashion assisted by the Su(z)12 C terminus. In addition to H3K4me3, PRC2 is inhibited by H3K36me2/3 (i.e., both H3K36me2 and H3K36me3). Direct PRC2 inhibition by H3K4me3 and H3K36me2/3 active marks is conserved in humans, mouse, and fly, rendering transcriptionally active chromatin refractory to PRC2 H3K27 trimethylation. While inhibition is present in plant PRC2, it can be modulated through exchange of the Su(z)12 subunit. Inhibition by active chromatin marks, coupled to stimulation by transcriptionally repressive H3K27me3, enables PRC2 to autonomously template repressive H3K27me3 without overwriting active chromatin domains.

Histone Methylation by PRC2 Is Inhibited by Active Chromatin Marks.,Schmitges FW, Prusty AB, Faty M, Stutzer A, Lingaraju GM, Aiwazian J, Sack R, Hess D, Li L, Zhou S, Bunker RD, Wirth U, Bouwmeester T, Bauer A, Ly-Hartig N, Zhao K, Chan H, Gu J, Gut H, Fischle W, Muller J, Thoma NH Mol Cell. 2011 May 6;42(3):330-41. PMID:21549310^[6]

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

References

↑ Tyler JK, Bulger M, Kamakaka RT, Kobayashi R, Kadonaga JT. The p55 subunit of Drosophila chromatin assembly factor 1 is homologous to a histone deacetylase-associated protein. Mol Cell Biol. 1996 Nov;16(11):6149-59. PMID:8887645
↑ Martinez-Balbas MA, Tsukiyama T, Gdula D, Wu C. Drosophila NURF-55, a WD repeat protein involved in histone metabolism. Proc Natl Acad Sci U S A. 1998 Jan 6;95(1):132-7. PMID:9419341
↑ Gdula DA, Sandaltzopoulos R, Tsukiyama T, Ossipow V, Wu C. Inorganic pyrophosphatase is a component of the Drosophila nucleosome remodeling factor complex. Genes Dev. 1998 Oct 15;12(20):3206-16. PMID:9784495
↑ Beall EL, Manak JR, Zhou S, Bell M, Lipsick JS, Botchan MR. Role for a Drosophila Myb-containing protein complex in site-specific DNA replication. Nature. 2002 Dec 19-26;420(6917):833-7. PMID:12490953 doi:10.1038/nature01228
↑ Taylor-Harding B, Binne UK, Korenjak M, Brehm A, Dyson NJ. p55, the Drosophila ortholog of RbAp46/RbAp48, is required for the repression of dE2F2/RBF-regulated genes. Mol Cell Biol. 2004 Oct;24(20):9124-36. PMID:15456884 doi:10.1128/MCB.24.20.9124-9136.2004
↑ Schmitges FW, Prusty AB, Faty M, Stutzer A, Lingaraju GM, Aiwazian J, Sack R, Hess D, Li L, Zhou S, Bunker RD, Wirth U, Bouwmeester T, Bauer A, Ly-Hartig N, Zhao K, Chan H, Gu J, Gut H, Fischle W, Muller J, Thoma NH. Histone Methylation by PRC2 Is Inhibited by Active Chromatin Marks. Mol Cell. 2011 May 6;42(3):330-41. PMID:21549310 doi:10.1016/j.molcel.2011.03.025

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/2yba"

@@ Line 3: / Line 3: @@
 <StructureSection load='2yba' size='340' side='right'caption='[[2yba]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2yba]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YBA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YBA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2yba]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YBA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YBA FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1kna|1kna]], [[1kne|1kne]], [[2xyi|2xyi]], [[2yb8|2yb8]]</div></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]] 2.55&#8491;</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=2yba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yba OCA], [https://pdbe.org/2yba PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yba RCSB], [https://www.ebi.ac.uk/pdbsum/2yba PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yba ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/CAF1_DROME CAF1_DROME]] Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA. Component of several complexes which regulate chromatin metabolism. These include the chromatin assembly factor 1 (CAF-1) complex, which is required for chromatin assembly following DNA replication and DNA repair; the nucleosome remodeling and deacetylase complex (the NuRD complex), which promotes transcriptional repression by histone deacetylation and nucleosome remodeling; the nucleosome remodeling factor (NURF) complex, which catalyzes ATP-dependent nucleosome sliding and facilitates transcription of chromatin; and the polycomb group (PcG) repressor complex ESC-E(Z), which promotes repression of homeotic genes during development. Also required for transcriptional repression of E2F target genes by E2f2 and Rbf or Rbf2.<ref>PMID:8887645</ref> <ref>PMID:9419341</ref> <ref>PMID:9784495</ref> <ref>PMID:12490953</ref> <ref>PMID:15456884</ref>
+[https://www.uniprot.org/uniprot/CAF1_DROME CAF1_DROME] Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA. Component of several complexes which regulate chromatin metabolism. These include the chromatin assembly factor 1 (CAF-1) complex, which is required for chromatin assembly following DNA replication and DNA repair; the nucleosome remodeling and deacetylase complex (the NuRD complex), which promotes transcriptional repression by histone deacetylation and nucleosome remodeling; the nucleosome remodeling factor (NURF) complex, which catalyzes ATP-dependent nucleosome sliding and facilitates transcription of chromatin; and the polycomb group (PcG) repressor complex ESC-E(Z), which promotes repression of homeotic genes during development. Also required for transcriptional repression of E2F target genes by E2f2 and Rbf or Rbf2.<ref>PMID:8887645</ref> <ref>PMID:9419341</ref> <ref>PMID:9784495</ref> <ref>PMID:12490953</ref> <ref>PMID:15456884</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Drome]]
+[[Category: Drosophila melanogaster]]
 [[Category: Large Structures]]
-[[Category: Aiwazian, J]]
+[[Category: Aiwazian J]]
-[[Category: Bauer, A]]
+[[Category: Bauer A]]
-[[Category: Bouwmeester, T]]
+[[Category: Bouwmeester T]]
-[[Category: Bunker, R D]]
+[[Category: Bunker RD]]
-[[Category: Chan, H]]
+[[Category: Chan H]]
-[[Category: Faty, M]]
+[[Category: Faty M]]
-[[Category: Fischle, W]]
+[[Category: Fischle W]]
-[[Category: Gu, J]]
+[[Category: Gu J]]
-[[Category: Gut, H]]
+[[Category: Gut H]]
-[[Category: Hess, D]]
+[[Category: Hess D]]
-[[Category: Li, L]]
+[[Category: Li L]]
-[[Category: Lingaraju, G M]]
+[[Category: Lingaraju GM]]
-[[Category: Ly-Hartig, N]]
+[[Category: Ly-Hartig N]]
-[[Category: Muller, J]]
+[[Category: Muller J]]
-[[Category: Prusty, A B]]
+[[Category: Prusty AB]]
-[[Category: Sack, R]]
+[[Category: Sack R]]
-[[Category: Schmitges, F W]]
+[[Category: Schmitges FW]]
-[[Category: Stutzer, A]]
+[[Category: Stutzer A]]
-[[Category: Thoma, N H]]
+[[Category: Thoma NH]]
-[[Category: Wirth, U]]
+[[Category: Wirth U]]
-[[Category: Zhao, K]]
+[[Category: Zhao K]]
-[[Category: Zhou, S]]
+[[Category: Zhou S]]
-[[Category: Chromatin remodelling]]
-[[Category: H3k4]]
-[[Category: Histone methylation h3k27]]
-[[Category: Polycomb]]
-[[Category: Prc2]]
-[[Category: Rbap46]]
-[[Category: Rbap48]]
-[[Category: Rbbp4]]
-[[Category: Rbbp7]]
-[[Category: Transcription]]
-[[Category: Wd40 domain]]

2yba

From Proteopedia

Revision as of 08:11, 23 August 2023

Crystal structure of Nurf55 in complex with histone H3

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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