3fk3

From Proteopedia

(Difference between revisions)

Current revision

Structure of the Yeats Domain, Yaf9

Structural highlights

3fk3 is a 3 chain structure with sequence from Saccharomyces cerevisiae. 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:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AF9_YEAST Component of the SWR1 complex which mediates the ATP-dependent exchange of histone H2A for the H2A variant HZT1 leading to transcriptional regulation of selected genes by chromatin remodeling. Component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histones H4 and H2A. The NuA4 complex is also involved in DNA repair. Yaf9 may also be required for viability in conditions in which the structural integrity of the spindle is compromised.^[1] ^[2] ^[3] ^[4] ^[5]

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

Chromatin can be modified by posttranslational modifications of histones, ATP-dependent remodeling, and incorporation of histone variants. The Saccharomyces cerevisiae protein Yaf9 is a subunit of both the essential histone acetyltransferase complex NuA4 and the ATP-dependent chromatin remodeling complex SWR1-C, which deposits histone variant H2A.Z into euchromatin. Yaf9 contains a YEATS domain, found in proteins associated with multiple chromatin-modifying enzymes and transcription complexes across eukaryotes. Here, we established the conservation of YEATS domain function from yeast to human, and determined the structure of this region from Yaf9 by x-ray crystallography to 2.3 A resolution. The Yaf9 YEATS domain consisted of a beta-sandwich characteristic of the Ig fold and contained three distinct conserved structural features. The structure of the Yaf9 YEATS domain was highly similar to that of the histone chaperone Asf1, a similarity that extended to an ability of Yaf9 to bind histones H3 and H4 in vitro. Using structure-function analysis, we found that the YEATS domain was required for Yaf9 function, histone variant H2A.Z chromatin deposition at specific promoters, and H2A.Z acetylation.

Asf1-like structure of the conserved Yaf9 YEATS domain and role in H2A.Z deposition and acetylation.,Wang AY, Schulze JM, Skordalakes E, Gin JW, Berger JM, Rine J, Kobor MS Proc Natl Acad Sci U S A. 2009 Dec 22;106(51):21573-8. Epub 2009 Dec 4. PMID:19966225^[6]

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

References

↑ Krogan NJ, Keogh MC, Datta N, Sawa C, Ryan OW, Ding H, Haw RA, Pootoolal J, Tong A, Canadien V, Richards DP, Wu X, Emili A, Hughes TR, Buratowski S, Greenblatt JF. A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol Cell. 2003 Dec;12(6):1565-76. PMID:14690608
↑ Le Masson I, Yu DY, Jensen K, Chevalier A, Courbeyrette R, Boulard Y, Smith MM, Mann C. Yaf9, a novel NuA4 histone acetyltransferase subunit, is required for the cellular response to spindle stress in yeast. Mol Cell Biol. 2003 Sep;23(17):6086-102. PMID:12917332
↑ Zhang H, Richardson DO, Roberts DN, Utley R, Erdjument-Bromage H, Tempst P, Cote J, Cairns BR. The Yaf9 component of the SWR1 and NuA4 complexes is required for proper gene expression, histone H4 acetylation, and Htz1 replacement near telomeres. Mol Cell Biol. 2004 Nov;24(21):9424-36. PMID:15485911 doi:24/21/9424
↑ 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
↑ Mizuguchi G, Shen X, Landry J, Wu WH, Sen S, Wu C. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science. 2004 Jan 16;303(5656):343-8. Epub 2003 Nov 26. PMID:14645854 doi:10.1126/science.1090701
↑ Wang AY, Schulze JM, Skordalakes E, Gin JW, Berger JM, Rine J, Kobor MS. Asf1-like structure of the conserved Yaf9 YEATS domain and role in H2A.Z deposition and acetylation. Proc Natl Acad Sci U S A. 2009 Dec 22;106(51):21573-8. Epub 2009 Dec 4. PMID:19966225

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3fk3"

@@ Line 3: / Line 3: @@
 <StructureSection load='3fk3' size='340' side='right'caption='[[3fk3]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3fk3]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FK3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FK3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3fk3]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FK3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FK3 FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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">N1966, YAF9, YNL107W ([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=MSE:SELENOMETHIONINE'>MSE</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=3fk3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fk3 OCA], [https://pdbe.org/3fk3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fk3 RCSB], [https://www.ebi.ac.uk/pdbsum/3fk3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fk3 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/AF9_YEAST AF9_YEAST]] Component of the SWR1 complex which mediates the ATP-dependent exchange of histone H2A for the H2A variant HZT1 leading to transcriptional regulation of selected genes by chromatin remodeling. Component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histones H4 and H2A. The NuA4 complex is also involved in DNA repair. Yaf9 may also be required for viability in conditions in which the structural integrity of the spindle is compromised.<ref>PMID:14690608</ref> <ref>PMID:12917332</ref> <ref>PMID:15485911</ref> <ref>PMID:15045029</ref> <ref>PMID:14645854</ref>
+[https://www.uniprot.org/uniprot/AF9_YEAST AF9_YEAST] Component of the SWR1 complex which mediates the ATP-dependent exchange of histone H2A for the H2A variant HZT1 leading to transcriptional regulation of selected genes by chromatin remodeling. Component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histones H4 and H2A. The NuA4 complex is also involved in DNA repair. Yaf9 may also be required for viability in conditions in which the structural integrity of the spindle is compromised.<ref>PMID:14690608</ref> <ref>PMID:12917332</ref> <ref>PMID:15485911</ref> <ref>PMID:15045029</ref> <ref>PMID:14645854</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 15: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fk/3fk3_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: Berger, J M]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Kobor, M S]]
+[[Category: Berger JM]]
-[[Category: Rine, J]]
+[[Category: Kobor MS]]
-[[Category: Schulze, J M]]
+[[Category: Rine J]]
-[[Category: Skordalakes, E]]
+[[Category: Schulze JM]]
-[[Category: Wang, A Y]]
+[[Category: Skordalakes E]]
-[[Category: Activator]]
+[[Category: Wang AY]]
-[[Category: Beta-sandwich]]
-[[Category: Chromatin regulator]]
-[[Category: Dna damage]]
-[[Category: Dna repair]]
-[[Category: Nucleus]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]

3fk3

From Proteopedia

Current revision

Structure of the Yeats Domain, Yaf9

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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