5nbn

From Proteopedia

(Difference between revisions)

Revision as of 07:45, 12 September 2018

Crystal structure of the Arp4-N-actin-Arp8-Ino80HSA module of INO80

Structural highlights

5nbn is a 8 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:	5nbm, 5nbl
Gene:	ARP4, ACT3, YJL081C, J1012 (Baker's yeast), ACT1, ABY1, END7, YFL039C (Baker's yeast), ARP8, YOR141C, YOR3348C (Baker's yeast), INO80, YGL150C, G1880 (Baker's yeast)
Activity:	DNA helicase, with EC number 3.6.4.12
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[INO80_YEAST] ATPase component of the INO80 complex which remodels chromatin by shifting nucleosomes and is involved in DNA repair (PubMed:10952318, PubMed:12887900). Its ability to induce transcription of some phosphate-responsive genes is modulated by inositol polyphosphates (PubMed:10952318, PubMed:10361278). The INO80 complex is involved in DNA repair by associating with 'Ser-129' phosphorylated H2A histones as a response to DNA damage (PubMed:15607974, PubMed:15607975).^[1] ^[2] ^[3] ^[4] ^[5] [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.^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13] ^[14] [ARP8_YEAST] Probably involved in transcription regulation via its interaction with the INO80 complex, a chromatin remodeling complex. Exhibits low basal ATPase activity, and unable to polymerize. Strongly prefer nucleosomes and H3-H4 tetramers over H2A-H2B dimers, suggesting it may act as a nucleosome recognition module within the complex.^[15] [ACT_YEAST] Actins are highly conserved proteins that are involved in various types of cell motility and are ubiquitously expressed in all eukaryotic cells.

Publication Abstract from PubMed

Nuclear actin (N-actin) and actin-related proteins (Arps) are critical components of several chromatin modulating complexes, including the chromatin remodeler INO80, but their function is largely elusive. Here, we report the crystal structure of the 180-kDa Arp8 module of Saccharomyces cerevisiae INO80 and establish its role in recognition of extranucleosomal linker DNA. Arp8 engages N-actin in a manner distinct from that of other actin-fold proteins and thereby specifies recruitment of the Arp4-N-actin heterodimer to a segmented scaffold of the helicase-SANT-associated (HSA) domain of Ino80. The helical HSA domain spans over 120 A and provides an extended binding platform for extranucleosomal entry DNA that is required for nucleosome sliding and genome-wide nucleosome positioning. Together with the recent cryo-electron microscopy structure of INO80(Core)-nucleosome complex, our findings suggest an allosteric mechanism by which INO80 senses 40-bp linker DNA to conduct highly processive chromatin remodeling.

The nuclear actin-containing Arp8 module is a linker DNA sensor driving INO80 chromatin remodeling.,Knoll KR, Eustermann S, Niebauer V, Oberbeckmann E, Stoehr G, Schall K, Tosi A, Schwarz M, Buchfellner A, Korber P, Hopfner KP Nat Struct Mol Biol. 2018 Sep;25(9):823-832. doi: 10.1038/s41594-018-0115-8. Epub, 2018 Sep 3. PMID:30177756^[16]

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

References

↑ Ebbert R, Birkmann A, Schuller HJ. The product of the SNF2/SWI2 paralogue INO80 of Saccharomyces cerevisiae required for efficient expression of various yeast structural genes is part of a high-molecular-weight protein complex. Mol Microbiol. 1999 May;32(4):741-51. PMID:10361278
↑ 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
↑ Shen X, Ranallo R, Choi E, Wu C. Involvement of actin-related proteins in ATP-dependent chromatin remodeling. Mol Cell. 2003 Jul;12(1):147-55. PMID:12887900
↑ Morrison AJ, Highland J, Krogan NJ, Arbel-Eden A, Greenblatt JF, Haber JE, Shen X. INO80 and gamma-H2AX interaction links ATP-dependent chromatin remodeling to DNA damage repair. Cell. 2004 Dec 17;119(6):767-75. doi: 10.1016/j.cell.2004.11.037. PMID:15607974 doi:http://dx.doi.org/10.1016/j.cell.2004.11.037
↑ van Attikum H, Fritsch O, Hohn B, Gasser SM. Recruitment of the INO80 complex by H2A phosphorylation links ATP-dependent chromatin remodeling with DNA double-strand break repair. Cell. 2004 Dec 17;119(6):777-88. doi: 10.1016/j.cell.2004.11.033. PMID:15607975 doi:http://dx.doi.org/10.1016/j.cell.2004.11.033
↑ 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
↑ Saravanan M, Wuerges J, Bose D, McCormack EA, Cook NJ, Zhang X, Wigley DB. Interactions between the nucleosome histone core and Arp8 in the INO80 chromatin remodeling complex. Proc Natl Acad Sci U S A. 2012 Dec 18;109(51):20883-8. doi:, 10.1073/pnas.1214735109. Epub 2012 Dec 3. PMID:23213201 doi:http://dx.doi.org/10.1073/pnas.1214735109
↑ Knoll KR, Eustermann S, Niebauer V, Oberbeckmann E, Stoehr G, Schall K, Tosi A, Schwarz M, Buchfellner A, Korber P, Hopfner KP. The nuclear actin-containing Arp8 module is a linker DNA sensor driving INO80 chromatin remodeling. Nat Struct Mol Biol. 2018 Sep;25(9):823-832. doi: 10.1038/s41594-018-0115-8. Epub, 2018 Sep 3. PMID:30177756 doi:http://dx.doi.org/10.1038/s41594-018-0115-8

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/5nbn"

@@ Line 3: / Line 3: @@
 <StructureSection load='5nbn' size='340' side='right' caption='[[5nbn]], [[Resolution|resolution]] 4.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5nbn]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NBN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NBN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5nbn]] is a 8 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=5NBN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NBN 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>, <scene name='pdbligand=LAR:LATRUNCULIN+A'>LAR</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=HIC:4-METHYL-HISTIDINE'>HIC</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5nbm|5nbm]], [[5nbl|5nbl]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ARP4, ACT3, YJL081C, J1012 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), ACT1, ABY1, END7, YFL039C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), ARP8, YOR141C, YOR3348C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), INO80, YGL150C, G1880 ([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/DNA_helicase DNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.12 3.6.4.12] </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=5nbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nbn OCA], [http://pdbe.org/5nbn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nbn RCSB], [http://www.ebi.ac.uk/pdbsum/5nbn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nbn ProSAT]</span></td></tr>
@@ Line 12: / Line 13: @@
 == Function ==
 [[http://www.uniprot.org/uniprot/INO80_YEAST INO80_YEAST]] ATPase component of the INO80 complex which remodels chromatin by shifting nucleosomes and is involved in DNA repair (PubMed:10952318, PubMed:12887900). Its ability to induce transcription of some phosphate-responsive genes is modulated by inositol polyphosphates (PubMed:10952318, PubMed:10361278). The INO80 complex is involved in DNA repair by associating with 'Ser-129' phosphorylated H2A histones as a response to DNA damage (PubMed:15607974, PubMed:15607975).<ref>PMID:10361278</ref> <ref>PMID:10952318</ref> <ref>PMID:12887900</ref> <ref>PMID:15607974</ref> <ref>PMID:15607975</ref>  [[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>  [[http://www.uniprot.org/uniprot/ARP8_YEAST ARP8_YEAST]] Probably involved in transcription regulation via its interaction with the INO80 complex, a chromatin remodeling complex. Exhibits low basal ATPase activity, and unable to polymerize. Strongly prefer nucleosomes and H3-H4 tetramers over H2A-H2B dimers, suggesting it may act as a nucleosome recognition module within the complex.<ref>PMID:23213201</ref>  [[http://www.uniprot.org/uniprot/ACT_YEAST ACT_YEAST]] Actins are highly conserved proteins that are involved in various types of cell motility and are ubiquitously expressed in all eukaryotic cells.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Nuclear actin (N-actin) and actin-related proteins (Arps) are critical components of several chromatin modulating complexes, including the chromatin remodeler INO80, but their function is largely elusive. Here, we report the crystal structure of the 180-kDa Arp8 module of Saccharomyces cerevisiae INO80 and establish its role in recognition of extranucleosomal linker DNA. Arp8 engages N-actin in a manner distinct from that of other actin-fold proteins and thereby specifies recruitment of the Arp4-N-actin heterodimer to a segmented scaffold of the helicase-SANT-associated (HSA) domain of Ino80. The helical HSA domain spans over 120 A and provides an extended binding platform for extranucleosomal entry DNA that is required for nucleosome sliding and genome-wide nucleosome positioning. Together with the recent cryo-electron microscopy structure of INO80(Core)-nucleosome complex, our findings suggest an allosteric mechanism by which INO80 senses 40-bp linker DNA to conduct highly processive chromatin remodeling.
+The nuclear actin-containing Arp8 module is a linker DNA sensor driving INO80 chromatin remodeling.,Knoll KR, Eustermann S, Niebauer V, Oberbeckmann E, Stoehr G, Schall K, Tosi A, Schwarz M, Buchfellner A, Korber P, Hopfner KP Nat Struct Mol Biol. 2018 Sep;25(9):823-832. doi: 10.1038/s41594-018-0115-8. Epub, 2018 Sep 3. PMID:30177756<ref>PMID:30177756</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 5nbn" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Baker's yeast]]
 [[Category: DNA helicase]]
 [[Category: Eustermann, S]]

5nbn

From Proteopedia

Revision as of 07:45, 12 September 2018

Crystal structure of the Arp4-N-actin-Arp8-Ino80HSA module of INO80

Structural highlights

Function

Publication Abstract from PubMed

References

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