5j9w

From Proteopedia

(Difference between revisions)

Revision as of 07:39, 10 June 2020

Crystal structure of the NuA4 core complex

Structural highlights

5j9w is a 12 chain structure with sequence from Baker's yeast. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Related:	5j9u, 5j9t, 5j9q
Gene:	ESA1, YOR244W, O5257 (Baker's yeast), EAF6, YJR082C, J1854 (Baker's yeast), EPL1, YFL024C (Baker's yeast), YNG2, EAF4, NBN1, YHR090C (Baker's yeast)
Activity:	Histone acetyltransferase, with EC number 2.3.1.48
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[YNG2_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. Involved in cell cycle progression and meiosis.^[1] ^[2] ^[3] ^[4] [ESA1_YEAST] Catalytic component of the NuA4 histone acetyltransferase (HAT) complex which is involved in epigenetic transcriptional activation of selected genes principally by acetylation of nucleosomal histones H4, H3, H2B, H2A and H2A variant H2A.Z. Acetylates histone H4 to form H4K5ac, H4K8ac, H4K12ac and H4K16ac, histone H3 to form H3K14ac, histone H2B to form H2BK16ac, histone H2A to form H2AK4ac and H2AK7ac, and histone variant H2A.Z to form H2A.ZK14ac. Acetylation of histone H4 is essential for DNA double-strand break repair through homologous recombination. Involved in cell cycle progression. Recruitment to promoters depends on H3K4me.^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13] [EPL1_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. Involved in gene silencing by neighboring heterochromatin, blockage of the silencing spreading along the chromosome, and required for cell cycle progression through G2/M.^[14] ^[15] ^[16] ^[17] [EAF6_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. Component of the NuA3 histone acetyltransferase complex, that acetylates Lys-14 of histone H3. Recruitment of NuA3 to nucleosomes requires methylated histone H3. In conjunction with the FACT complex, NuA3 may be involved in transcriptional regulation.^[18]

Publication Abstract from PubMed

NuA4 catalyzes the acetylation of nucleosomes at histone H4, which is a well-established epigenetic event, controlling many genomic processes in Saccharomyces cerevisiae. Here we report the crystal structures of the NuA4 core complex and a cryoelectron microscopy structure with the nucleosome. The structures show that the histone-binding pocket of the enzyme is rearranged, suggesting its activation. The enzyme binds the histone tail mainly through the target lysine residue, with a preference for a small residue at the -1 position. The complex engages the nucleosome at the dish face and orients its catalytic pocket close to the H4 tail to achieve selective acetylation. The combined data reveal a space-sequence double recognition mechanism of the histone tails by a modifying enzyme in the context of the nucleosome.

The NuA4 Core Complex Acetylates Nucleosomal Histone H4 through a Double Recognition Mechanism.,Xu P, Li C, Chen Z, Jiang S, Fan S, Wang J, Dai J, Zhu P, Chen Z Mol Cell. 2016 Sep 15;63(6):965-75. doi: 10.1016/j.molcel.2016.07.024. Epub 2016 , Sep 1. PMID:27594449^[19]

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

References

↑ Loewith R, Meijer M, Lees-Miller SP, Riabowol K, Young D. Three yeast proteins related to the human candidate tumor suppressor p33(ING1) are associated with histone acetyltransferase activities. Mol Cell Biol. 2000 Jun;20(11):3807-16. PMID:10805724
↑ Choy JS, Tobe BT, Huh JH, Kron SJ. Yng2p-dependent NuA4 histone H4 acetylation activity is required for mitotic and meiotic progression. J Biol Chem. 2001 Nov 23;276(47):43653-62. Epub 2001 Sep 5. PMID:11544250 doi:http://dx.doi.org/10.1074/jbc.M102531200
↑ Nourani A, Doyon Y, Utley RT, Allard S, Lane WS, Cote J. Role of an ING1 growth regulator in transcriptional activation and targeted histone acetylation by the NuA4 complex. Mol Cell Biol. 2001 Nov;21(22):7629-40. PMID:11604499 doi:http://dx.doi.org/10.1128/MCB.21.22.7629-7640.2001
↑ Choy JS, Kron SJ. NuA4 subunit Yng2 function in intra-S-phase DNA damage response. Mol Cell Biol. 2002 Dec;22(23):8215-25. PMID:12417725
↑ Ikeda K, Steger DJ, Eberharter A, Workman JL. Activation domain-specific and general transcription stimulation by native histone acetyltransferase complexes. Mol Cell Biol. 1999 Jan;19(1):855-63. PMID:9858608
↑ Clarke AS, Lowell JE, Jacobson SJ, Pillus L. Esa1p is an essential histone acetyltransferase required for cell cycle progression. Mol Cell Biol. 1999 Apr;19(4):2515-26. PMID:10082517
↑ Vignali M, Steger DJ, Neely KE, Workman JL. Distribution of acetylated histones resulting from Gal4-VP16 recruitment of SAGA and NuA4 complexes. EMBO J. 2000 Jun 1;19(11):2629-40. PMID:10835360 doi:http://dx.doi.org/10.1093/emboj/19.11.2629
↑ Galarneau L, Nourani A, Boudreault AA, Zhang Y, Heliot L, Allard S, Savard J, Lane WS, Stillman DJ, Cote J. Multiple links between the NuA4 histone acetyltransferase complex and epigenetic control of transcription. Mol Cell. 2000 Jun;5(6):927-37. PMID:10911987
↑ Bird AW, Yu DY, Pray-Grant MG, Qiu Q, Harmon KE, Megee PC, Grant PA, Smith MM, Christman MF. Acetylation of histone H4 by Esa1 is required for DNA double-strand break repair. Nature. 2002 Sep 26;419(6905):411-5. PMID:12353039 doi:http://dx.doi.org/10.1038/nature01035
↑ Nourani A, Utley RT, Allard S, Cote J. Recruitment of the NuA4 complex poises the PHO5 promoter for chromatin remodeling and activation. EMBO J. 2004 Jul 7;23(13):2597-607. Epub 2004 Jun 3. PMID:15175650 doi:http://dx.doi.org/10.1038/sj.emboj.7600230
↑ Robert F, Pokholok DK, Hannett NM, Rinaldi NJ, Chandy M, Rolfe A, Workman JL, Gifford DK, Young RA. Global position and recruitment of HATs and HDACs in the yeast genome. Mol Cell. 2004 Oct 22;16(2):199-209. PMID:15494307 doi:http://dx.doi.org/10.1016/j.molcel.2004.09.021
↑ 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
↑ Tamburini BA, Tyler JK. Localized histone acetylation and deacetylation triggered by the homologous recombination pathway of double-strand DNA repair. Mol Cell Biol. 2005 Jun;25(12):4903-13. PMID:15923609 doi:http://dx.doi.org/25/12/4903
↑ Galarneau L, Nourani A, Boudreault AA, Zhang Y, Heliot L, Allard S, Savard J, Lane WS, Stillman DJ, Cote J. Multiple links between the NuA4 histone acetyltransferase complex and epigenetic control of transcription. Mol Cell. 2000 Jun;5(6):927-37. PMID:10911987
↑ Boudreault AA, Cronier D, Selleck W, Lacoste N, Utley RT, Allard S, Savard J, Lane WS, Tan S, Cote J. Yeast enhancer of polycomb defines global Esa1-dependent acetylation of chromatin. Genes Dev. 2003 Jun 1;17(11):1415-28. PMID:12782659 doi:http://dx.doi.org/10.1101/gad.1056603
↑ Oki M, Valenzuela L, Chiba T, Ito T, Kamakaka RT. Barrier proteins remodel and modify chromatin to restrict silenced domains. Mol Cell Biol. 2004 Mar;24(5):1956-67. PMID:14966276
↑ 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
↑ Taverna SD, Ilin S, Rogers RS, Tanny JC, Lavender H, Li H, Baker L, Boyle J, Blair LP, Chait BT, Patel DJ, Aitchison JD, Tackett AJ, Allis CD. Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs. Mol Cell. 2006 Dec 8;24(5):785-96. PMID:17157260 doi:http://dx.doi.org/10.1016/j.molcel.2006.10.026
↑ Xu P, Li C, Chen Z, Jiang S, Fan S, Wang J, Dai J, Zhu P, Chen Z. The NuA4 Core Complex Acetylates Nucleosomal Histone H4 through a Double Recognition Mechanism. Mol Cell. 2016 Sep 15;63(6):965-75. doi: 10.1016/j.molcel.2016.07.024. Epub 2016 , Sep 1. PMID:27594449 doi:http://dx.doi.org/10.1016/j.molcel.2016.07.024

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/5j9w"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the NuA4 core complex==
-<StructureSection load='5j9w' size='340' side='right' caption='[[5j9w]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='5j9w' size='340' side='right'caption='[[5j9w]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5j9w]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J9W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J9W FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5j9w]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J9W OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5J9W FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACO:ACETYL+COENZYME+*A'>ACO</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACO:ACETYL+COENZYME+*A'>ACO</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5j9u|5j9u]], [[5j9t|5j9t]], [[5j9q|5j9q]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ESA1, YOR244W, O5257 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), EAF6, YJR082C, J1854 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), EPL1, YFL024C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), YNG2, EAF4, NBN1, YHR090C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_acetyltransferase Histone acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.48 2.3.1.48] </span></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=5j9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j9w OCA], [http://pdbe.org/5j9w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j9w RCSB], [http://www.ebi.ac.uk/pdbsum/5j9w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j9w ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5j9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j9w OCA], [http://pdbe.org/5j9w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j9w RCSB], [http://www.ebi.ac.uk/pdbsum/5j9w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j9w ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 21: / Line 22: @@
 </div>
 <div class="pdbe-citations 5j9w" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Histone acetyltransferase 3D structures|Histone acetyltransferase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Baker's yeast]]
 [[Category: Histone acetyltransferase]]
+[[Category: Large Structures]]
 [[Category: Chen, Z C]]
 [[Category: Xu, P]]

5j9w

From Proteopedia

Revision as of 07:39, 10 June 2020

Crystal structure of the NuA4 core complex

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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