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3tvv

From Proteopedia

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Revision as of 08:17, 6 December 2023

Structure of the tandem PH domains of Rtt106 (residues 68-315)

Structural highlights

3tvv is a 2 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.589Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RT106_YEAST Histones H3 and H4 chaperone involved in the nucleosome formation and heterochromatin silencing. Required for the deposition of H3K56ac-carrying H3-H4 complex onto newly-replicated DNA. Plays a role in the transcriptional regulation of the cell-cycle dependent histone genes by directly recruiting the SWI/SNF and RSC chromatin remodeling complexes to the histone genes in a cell cycle dependent manner. In cooperation with HIR and ASF1, creates a repressive structure at the core histone gene promoter and contributes to their repression outside of S phase. Involved in regulation of Ty1 transposition.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12]

Publication Abstract from PubMed

Dynamic variations in the structure of chromatin influence virtually all DNA-related processes in eukaryotes and are controlled in part by post-translational modifications of histones. One such modification, the acetylation of lysine 56 (H3K56ac) in the amino-terminal alpha-helix (alphaN) of histone H3, has been implicated in the regulation of nucleosome assembly during DNA replication and repair, and nucleosome disassembly during gene transcription. In Saccharomyces cerevisiae, the histone chaperone Rtt106 contributes to the deposition of newly synthesized H3K56ac-carrying H3-H4 complex on replicating DNA, but it is unclear how Rtt106 binds H3-H4 and specifically recognizes H3K56ac as there is no apparent acetylated lysine reader domain in Rtt106. Here, we show that two domains of Rtt106 are involved in a combinatorial recognition of H3-H4. An N-terminal domain homodimerizes and interacts with H3-H4 independently of acetylation while a double pleckstrin-homology (PH) domain binds the K56-containing region of H3. Affinity is markedly enhanced upon acetylation of K56, an effect that is probably due to increased conformational entropy of the alphaN helix of H3. Our data support a mode of interaction where the N-terminal homodimeric domain of Rtt106 intercalates between the two H3-H4 components of the (H3-H4)(2) tetramer while two double PH domains in the Rtt106 dimer interact with each of the two H3K56ac sites in (H3-H4)(2). We show that the Rtt106-(H3-H4)(2) interaction is important for gene silencing and the DNA damage response.

Structural basis for recognition of H3K56-acetylated histone H3-H4 by the chaperone Rtt106.,Su D, Hu Q, Li Q, Thompson JR, Cui G, Fazly A, Davies BA, Botuyan MV, Zhang Z, Mer G Nature. 2012 Feb 5. doi: 10.1038/nature10861. PMID:22307274^[13]

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

References

↑ Scholes DT, Banerjee M, Bowen B, Curcio MJ. Multiple regulators of Ty1 transposition in Saccharomyces cerevisiae have conserved roles in genome maintenance. Genetics. 2001 Dec;159(4):1449-65. PMID:11779788
↑ Huang S, Zhou H, Katzmann D, Hochstrasser M, Atanasova E, Zhang Z. Rtt106p is a histone chaperone involved in heterochromatin-mediated silencing. Proc Natl Acad Sci U S A. 2005 Sep 20;102(38):13410-5. Epub 2005 Sep 12. PMID:16157874 doi:http://dx.doi.org/0506176102
↑ Huang S, Zhou H, Tarara J, Zhang Z. A novel role for histone chaperones CAF-1 and Rtt106p in heterochromatin silencing. EMBO J. 2007 May 2;26(9):2274-83. Epub 2007 Apr 5. PMID:17410207 doi:http://dx.doi.org/7601670
↑ Fillingham J, Kainth P, Lambert JP, van Bakel H, Tsui K, Pena-Castillo L, Nislow C, Figeys D, Hughes TR, Greenblatt J, Andrews BJ. Two-color cell array screen reveals interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene repression. Mol Cell. 2009 Aug 14;35(3):340-51. PMID:19683497 doi:http://dx.doi.org/S1097-2765(09)00461-4
↑ Burgess RJ, Zhou H, Han J, Zhang Z. A role for Gcn5 in replication-coupled nucleosome assembly. Mol Cell. 2010 Feb 26;37(4):469-80. doi: 10.1016/j.molcel.2010.01.020. PMID:20188666 doi:http://dx.doi.org/10.1016/j.molcel.2010.01.020
↑ Wan Y, Chen W, Xing J, Tan J, Li B, Chen H, Lin Z, Chiang JH, Saleem RA. Transcriptome profiling reveals a novel role for trichostatin A in antagonizing histone chaperone Chz1 mediated telomere anti-silencing. FEBS Lett. 2011 Aug 4;585(15):2519-25. doi: 10.1016/j.febslet.2011.06.036. Epub, 2011 Jul 14. PMID:21763693 doi:http://dx.doi.org/10.1016/j.febslet.2011.06.036
↑ Kurat CF, Lambert JP, van Dyk D, Tsui K, van Bakel H, Kaluarachchi S, Friesen H, Kainth P, Nislow C, Figeys D, Fillingham J, Andrews BJ. Restriction of histone gene transcription to S phase by phosphorylation of a chromatin boundary protein. Genes Dev. 2011 Dec 1;25(23):2489-501. doi: 10.1101/gad.173427.111. PMID:22156209 doi:http://dx.doi.org/10.1101/gad.173427.111
↑ Yu Y, Srinivasan M, Nakanishi S, Leatherwood J, Shilatifard A, Sternglanz R. A conserved patch near the C terminus of histone H4 is required for genome stability in budding yeast. Mol Cell Biol. 2011 Jun;31(11):2311-25. doi: 10.1128/MCB.01432-10. Epub 2011 Mar , 28. PMID:21444721 doi:http://dx.doi.org/10.1128/MCB.01432-10
↑ Ferreira ME, Flaherty K, Prochasson P. The Saccharomyces cerevisiae histone chaperone Rtt106 mediates the cell cycle recruitment of SWI/SNF and RSC to the HIR-dependent histone genes. PLoS One. 2011;6(6):e21113. doi: 10.1371/journal.pone.0021113. Epub 2011 Jun 15. PMID:21698254 doi:http://dx.doi.org/10.1371/journal.pone.0021113
↑ Amin AD, Dimova DK, Ferreira ME, Vishnoi N, Hancock LC, Osley MA, Prochasson P. The mitotic Clb cyclins are required to alleviate HIR-mediated repression of the yeast histone genes at the G1/S transition. Biochim Biophys Acta. 2012 Jan;1819(1):16-27. doi: 10.1016/j.bbagrm.2011.09.003. , Epub 2011 Sep 28. PMID:21978826 doi:http://dx.doi.org/10.1016/j.bbagrm.2011.09.003
↑ Silva AC, Xu X, Kim HS, Fillingham J, Kislinger T, Mennella TA, Keogh MC. The replication-independent histone H3-H4 chaperones HIR, ASF1, and RTT106 co-operate to maintain promoter fidelity. J Biol Chem. 2012 Jan 13;287(3):1709-18. doi: 10.1074/jbc.M111.316489. Epub 2011 , Nov 29. PMID:22128187 doi:http://dx.doi.org/10.1074/jbc.M111.316489
↑ Liu Y, Huang H, Zhou BO, Wang SS, Hu Y, Li X, Liu J, Zang J, Niu L, Wu J, Zhou JQ, Teng M, Shi Y. Structural analysis of Rtt106p reveals a DNA binding role required for heterochromatin silencing. J Biol Chem. 2010 Feb 5;285(6):4251-62. Epub 2009 Dec 10. PMID:20007951 doi:10.1074/jbc.M109.055996
↑ Su D, Hu Q, Li Q, Thompson JR, Cui G, Fazly A, Davies BA, Botuyan MV, Zhang Z, Mer G. Structural basis for recognition of H3K56-acetylated histone H3-H4 by the chaperone Rtt106. Nature. 2012 Feb 5. doi: 10.1038/nature10861. PMID:22307274 doi:10.1038/nature10861

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/3tvv"

Categories: Large Structures | Saccharomyces cerevisiae S288C | Mer G | Su D | Thompson JR

@@ Line 3: / Line 3: @@
 <StructureSection load='3tvv' size='340' side='right'caption='[[3tvv]], [[Resolution|resolution]] 2.59&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3tvv]] is a 2 chain structure with sequence from [https://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=3TVV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TVV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3tvv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TVV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TVV 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]] 2.589&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3fss|3fss]], [[3hkh|3hkh]], [[3tw1|3tw1]]</div></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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">N1346, RTT106, YNL206C ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=3tvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tvv OCA], [https://pdbe.org/3tvv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tvv RCSB], [https://www.ebi.ac.uk/pdbsum/3tvv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tvv ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RT106_YEAST RT106_YEAST]] Histones H3 and H4 chaperone involved in the nucleosome formation and heterochromatin silencing. Required for the deposition of H3K56ac-carrying H3-H4 complex onto newly-replicated DNA. Plays a role in the transcriptional regulation of the cell-cycle dependent histone genes by directly recruiting the SWI/SNF and RSC chromatin remodeling complexes to the histone genes in a cell cycle dependent manner. In cooperation with HIR and ASF1, creates a repressive structure at the core histone gene promoter and contributes to their repression outside of S phase. Involved in regulation of Ty1 transposition.<ref>PMID:11779788</ref> <ref>PMID:16157874</ref> <ref>PMID:17410207</ref> <ref>PMID:19683497</ref> <ref>PMID:20188666</ref> <ref>PMID:21763693</ref> <ref>PMID:22156209</ref> <ref>PMID:21444721</ref> <ref>PMID:21698254</ref> <ref>PMID:21978826</ref> <ref>PMID:22128187</ref> <ref>PMID:20007951</ref>
+[https://www.uniprot.org/uniprot/RT106_YEAST RT106_YEAST] Histones H3 and H4 chaperone involved in the nucleosome formation and heterochromatin silencing. Required for the deposition of H3K56ac-carrying H3-H4 complex onto newly-replicated DNA. Plays a role in the transcriptional regulation of the cell-cycle dependent histone genes by directly recruiting the SWI/SNF and RSC chromatin remodeling complexes to the histone genes in a cell cycle dependent manner. In cooperation with HIR and ASF1, creates a repressive structure at the core histone gene promoter and contributes to their repression outside of S phase. Involved in regulation of Ty1 transposition.<ref>PMID:11779788</ref> <ref>PMID:16157874</ref> <ref>PMID:17410207</ref> <ref>PMID:19683497</ref> <ref>PMID:20188666</ref> <ref>PMID:21763693</ref> <ref>PMID:22156209</ref> <ref>PMID:21444721</ref> <ref>PMID:21698254</ref> <ref>PMID:21978826</ref> <ref>PMID:22128187</ref> <ref>PMID:20007951</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Baker's yeast]]
 [[Category: Large Structures]]
-[[Category: Mer, G]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Su, D]]
+[[Category: Mer G]]
-[[Category: Thompson, J R]]
+[[Category: Su D]]
-[[Category: Chaperone]]
+[[Category: Thompson JR]]
-[[Category: Chromosomal protein]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Tandem pleckstrin-homology domain]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]

3tvv

From Proteopedia

Revision as of 08:17, 6 December 2023

Structure of the tandem PH domains of Rtt106 (residues 68-315)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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