2k3y: Difference between revisions

Revision as of 08:33, 15 November 2023

Solution structure of EAF3 chromo barrel domain bound to histone h3 with a dimethyllysine analog H3K36ME2

Structural highlights

2k3y is a 1 chain structure with sequence from Saccharomyces cerevisiae. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Ligands:	M2L
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

EAF3_YEAST Component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A. The NuA4 complex is also involved in DNA repair.^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Deacetylation of nucleosomes by the Rpd3S histone deacetylase along the path of transcribing RNA polymerase II regulates access to DNA, contributing to faithful gene transcription. The association of Rpd3S with chromatin requires its Eaf3 subunit, which binds histone H3 methylated at lysine 36 (H3K36). Eaf3 is also part of NuA4 acetyltransferase that recognizes methylated H3K4. Here we show that Eaf3 in Saccharomyces cerevisiae contains a chromo barrel-related domain that binds methylated peptides, including H3K36 and H3K4, with low specificity and millimolar-range affinity. Nuclear magnetic resonance structure determination of Eaf3 bound to methylated H3K36 was accomplished by engineering a linked Eaf3-H3K36 molecule with a chemically incorporated methyllysine analog. Our study uncovers the molecular details of Eaf3-methylated H3K36 complex formation, and suggests that, in the cell, Eaf3 can only function within a framework of combinatorial interactions. This work also provides a general method for structure determination of low-affinity protein complexes implicated in methyllysine recognition.

Structural basis for the recognition of methylated histone H3K36 by the Eaf3 subunit of histone deacetylase complex Rpd3S.,Xu C, Cui G, Botuyan MV, Mer G Structure. 2008 Nov 12;16(11):1740-50. Epub 2008 Sep 25. PMID:18818090^[4]

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

References

↑ Eisen A, Utley RT, Nourani A, Allard S, Schmidt P, Lane WS, Lucchesi JC, Cote J. The yeast NuA4 and Drosophila MSL complexes contain homologous subunits important for transcription regulation. J Biol Chem. 2001 Feb 2;276(5):3484-91. Epub 2000 Oct 17. PMID:11036083 doi:https://dx.doi.org/10.1074/jbc.M008159200
↑ Reid JL, Moqtaderi Z, Struhl K. Eaf3 regulates the global pattern of histone acetylation in Saccharomyces cerevisiae. Mol Cell Biol. 2004 Jan;24(2):757-64. PMID:14701747
↑ Kobor MS, Venkatasubrahmanyam S, Meneghini MD, Gin JW, Jennings JL, Link AJ, Madhani HD, Rine J. A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. PLoS Biol. 2004 May;2(5):E131. Epub 2004 Mar 23. PMID:15045029 doi:10.1371/journal.pbio.0020131
↑ Xu C, Cui G, Botuyan MV, Mer G. Structural basis for the recognition of methylated histone H3K36 by the Eaf3 subunit of histone deacetylase complex Rpd3S. Structure. 2008 Nov 12;16(11):1740-50. Epub 2008 Sep 25. PMID:18818090 doi:10.1016/j.str.2008.08.008

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OCA

[1] Eisen A, Utley RT, Nourani A, Allard S, Schmidt P, Lane WS, Lucchesi JC, Cote J. The yeast NuA4 and Drosophila MSL complexes contain homologous subunits important for transcription regulation. J Biol Chem. 2001 Feb 2;276(5):3484-91. Epub 2000 Oct 17. PMID:11036083 doi:https://dx.doi.org/10.1074/jbc.M008159200

[2] Reid JL, Moqtaderi Z, Struhl K. Eaf3 regulates the global pattern of histone acetylation in Saccharomyces cerevisiae. Mol Cell Biol. 2004 Jan;24(2):757-64. PMID:14701747

[3] Kobor MS, Venkatasubrahmanyam S, Meneghini MD, Gin JW, Jennings JL, Link AJ, Madhani HD, Rine J. A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. PLoS Biol. 2004 May;2(5):E131. Epub 2004 Mar 23. PMID:15045029 doi:10.1371/journal.pbio.0020131

[4] Xu C, Cui G, Botuyan MV, Mer G. Structural basis for the recognition of methylated histone H3K36 by the Eaf3 subunit of histone deacetylase complex Rpd3S. Structure. 2008 Nov 12;16(11):1740-50. Epub 2008 Sep 25. PMID:18818090 doi:10.1016/j.str.2008.08.008

[1]

[2]

[3]

[4]

@@ Line 1: / Line 1: @@
 ==Solution structure of EAF3 chromo barrel domain bound to histone h3 with a dimethyllysine analog H3K36ME2==
-<StructureSection load='2k3y' size='340' side='right'caption='[[2k3y]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2k3y' size='340' side='right'caption='[[2k3y]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2k3y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K3Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2K3Y FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2k3y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K3Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2K3Y FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M2L:(2R)-2-AMINO-3-(2-DIMETHYLAMINOETHYLSULFANYL)PROPANOIC+ACID'>M2L</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">EAF3, YPR023C, YP9367.03C ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=M2L:(2R)-2-AMINO-3-(2-DIMETHYLAMINOETHYLSULFANYL)PROPANOIC+ACID'>M2L</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=2k3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k3y OCA], [https://pdbe.org/2k3y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2k3y RCSB], [https://www.ebi.ac.uk/pdbsum/2k3y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2k3y ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/EAF3_YEAST EAF3_YEAST]] Component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A. The NuA4 complex is also involved in DNA repair.<ref>PMID:11036083</ref> <ref>PMID:14701747</ref> <ref>PMID:15045029</ref>
+[https://www.uniprot.org/uniprot/EAF3_YEAST EAF3_YEAST] Component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A. The NuA4 complex is also involved in DNA repair.<ref>PMID:11036083</ref> <ref>PMID:14701747</ref> <ref>PMID:15045029</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: Mer, G]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Xu, C]]
+[[Category: Mer G]]
-[[Category: Chromatin regulator]]
+[[Category: Xu C]]
-[[Category: Chromo barrel domain]]
-[[Category: Chromosomal protein]]
-[[Category: Dimethylated histone h3k36]]
-[[Category: Dna damage]]
-[[Category: Dna repair]]
-[[Category: Dna-binding]]
-[[Category: Eaf3]]
-[[Category: Eaf3-h3k36me2 fusion]]
-[[Category: Histone deacetylase]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-[[Category: Transcription regulator]]

2k3y: Difference between revisions

Revision as of 08:33, 15 November 2023

Solution structure of EAF3 chromo barrel domain bound to histone h3 with a dimethyllysine analog H3K36ME2

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

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