3qb0

From Proteopedia

(Difference between revisions)

Revision as of 06:00, 8 June 2022

Crystal structure of Actin-related protein Arp4 from S. cerevisiae complexed with ATP

Structural highlights

3qb0 is a 4 chain structure with sequence from Atcc 18824. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Gene:	ACT3, ARP4, J1012, YJL081C (ATCC 18824)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[ARP4_YEAST] Chromatin interaction 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. ARP4 recognizes H2AS128ph (gamma-H2A) and is required for NuA4 complex integrity. 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 INO80 complex which remodels chromatin by shifting nucleosomes. Its ability to induce transcription of some phosphate-responsive genes is modulated by inositol polyphosphates. The INO80 complex is involved in DNA repair by associating to gamma-H2A as a response to DNA damage.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9]

Publication Abstract from PubMed

Nuclear actin and actin-related proteins (Arps) are integral components of various chromatin-remodelling complexes. Actin in such nuclear assemblies does not form filaments but associates in defined complexes, for instance with Arp4 and Arp8 in the INO80 remodeller. To understand the relationship between nuclear actin and its associated Arps and to test the possibility that Arp4 and Arp8 help maintain actin in defined states, we structurally analysed Arp4 and Arp8 from Saccharomyces cerevisiae and tested their biochemical effects on actin assembly and disassembly. The solution structures of isolated Arp4 and Arp8 indicate them to be monomeric and the crystal structure of ATP-Arp4 reveals several differences to actin that explain why Arp4 does not form filaments itself. Remarkably, Arp4, assisted by Arp8, influences actin polymerization in vitro and is able to depolymerize actin filaments. Arp4 likely forms a complex with monomeric actin via the barbed end. Our data thus help explaining how nuclear actin is held in a discrete complex within the INO80 chromatin remodeller.

Structural biochemistry of nuclear actin-related proteins 4 and 8 reveals their interaction with actin.,Fenn S, Breitsprecher D, Gerhold CB, Witte G, Faix J, Hopfner KP EMBO J. 2011 Apr 15. PMID:21499228^[10]

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

References

↑ 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
↑ Shen X, Mizuguchi G, Hamiche A, Wu C. A chromatin remodelling complex involved in transcription and DNA processing. Nature. 2000 Aug 3;406(6795):541-4. PMID:10952318 doi:http://dx.doi.org/10.1038/35020123
↑ Harata M, Zhang Y, Stillman DJ, Matsui D, Oma Y, Nishimori K, Mochizuki R. Correlation between chromatin association and transcriptional regulation for the Act3p/Arp4 nuclear actin-related protein of Saccharomyces cerevisiae. Nucleic Acids Res. 2002 Apr 15;30(8):1743-50. PMID:11937627
↑ 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
↑ Gorzer I, Schuller C, Heidenreich E, Krupanska L, Kuchler K, Wintersberger U. The nuclear actin-related protein Act3p/Arp4p of Saccharomyces cerevisiae is involved in transcription regulation of stress genes. Mol Microbiol. 2003 Nov;50(4):1155-71. PMID:14622406
↑ 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
↑ 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
↑ 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
↑ Downs JA, Allard S, Jobin-Robitaille O, Javaheri A, Auger A, Bouchard N, Kron SJ, Jackson SP, Cote J. Binding of chromatin-modifying activities to phosphorylated histone H2A at DNA damage sites. Mol Cell. 2004 Dec 22;16(6):979-90. PMID:15610740 doi:http://dx.doi.org/S1097276504007580
↑ Fenn S, Breitsprecher D, Gerhold CB, Witte G, Faix J, Hopfner KP. Structural biochemistry of nuclear actin-related proteins 4 and 8 reveals their interaction with actin. EMBO J. 2011 Apr 15. PMID:21499228 doi:10.1038/emboj.2011.118

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/3qb0"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Actin-related protein Arp4 from S. cerevisiae complexed with ATP==
-<StructureSection load='3qb0' size='340' side='right' caption='[[3qb0]], [[Resolution|resolution]] 3.40&Aring;' scene=''>
+<StructureSection load='3qb0' size='340' side='right'caption='[[3qb0]], [[Resolution|resolution]] 3.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3qb0]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QB0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QB0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3qb0]] is a 4 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=3QB0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QB0 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ACT3, ARP4, J1012, YJL081C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ACT3, ARP4, J1012, YJL081C ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=3qb0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qb0 OCA], [http://pdbe.org/3qb0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3qb0 RCSB], [http://www.ebi.ac.uk/pdbsum/3qb0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3qb0 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=3qb0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qb0 OCA], [https://pdbe.org/3qb0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qb0 RCSB], [https://www.ebi.ac.uk/pdbsum/3qb0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qb0 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ARP4_YEAST ARP4_YEAST]] Chromatin interaction 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. ARP4 recognizes H2AS128ph (gamma-H2A) and is required for NuA4 complex integrity. 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 INO80 complex which remodels chromatin by shifting nucleosomes. Its ability to induce transcription of some phosphate-responsive genes is modulated by inositol polyphosphates. The INO80 complex is involved in DNA repair by associating to gamma-H2A as a response to DNA damage.<ref>PMID:10911987</ref> <ref>PMID:10952318</ref> <ref>PMID:11937627</ref> <ref>PMID:12353039</ref> <ref>PMID:14622406</ref> <ref>PMID:14645854</ref> <ref>PMID:14690608</ref> <ref>PMID:15045029</ref> <ref>PMID:15610740</ref>
+[[https://www.uniprot.org/uniprot/ARP4_YEAST ARP4_YEAST]] Chromatin interaction 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. ARP4 recognizes H2AS128ph (gamma-H2A) and is required for NuA4 complex integrity. 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 INO80 complex which remodels chromatin by shifting nucleosomes. Its ability to induce transcription of some phosphate-responsive genes is modulated by inositol polyphosphates. The INO80 complex is involved in DNA repair by associating to gamma-H2A as a response to DNA damage.<ref>PMID:10911987</ref> <ref>PMID:10952318</ref> <ref>PMID:11937627</ref> <ref>PMID:12353039</ref> <ref>PMID:14622406</ref> <ref>PMID:14645854</ref> <ref>PMID:14690608</ref> <ref>PMID:15045029</ref> <ref>PMID:15610740</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 24: @@
 </StructureSection>
 [[Category: Atcc 18824]]
+[[Category: Large Structures]]
 [[Category: Breitsprecher, D]]
 [[Category: Faix, J]]

3qb0

From Proteopedia

Revision as of 06:00, 8 June 2022

Crystal structure of Actin-related protein Arp4 from S. cerevisiae complexed with ATP

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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