3gyp

From Proteopedia

(Difference between revisions)

Current revision

Rtt106p

Structural highlights

3gyp is a 1 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 2.406Å
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]

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

Rtt106p is a Saccharomyces cerevisiae histone chaperone with roles in heterochromatin silencing and nucleosome assembly. The molecular mechanism by which Rtt106p engages in chromatin dynamics remains unclear. Here, we report the 2.5 A crystal structure of the core domain of Rtt106p, which adopts an unusual "double pleckstrin homology" domain architecture that represents a novel structural mode for histone chaperones. A histone H3-H4-binding region and a novel double-stranded DNA-binding region have been identified. Mutagenesis studies reveal that the histone and DNA binding activities of Rtt106p are involved in Sir protein-mediated heterochromatin formation. Our results uncover the structural basis of the diverse functions of Rtt106p and provide new insights into its cellular roles.

Structural analysis of Rtt106p reveals a DNA binding role required for heterochromatin silencing.,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 J Biol Chem. 2010 Feb 5;285(6):4251-62. Epub 2009 Dec 10. PMID:20007951^[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
↑ 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

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/3gyp"

@@ Line 1: / Line 1: @@
 ==Rtt106p==
-<StructureSection load='3gyp' size='340' side='right' caption='[[3gyp]], [[Resolution|resolution]] 2.41&Aring;' scene=''>
+<StructureSection load='3gyp' size='340' side='right'caption='[[3gyp]], [[Resolution|resolution]] 2.41&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3gyp]] is a 1 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=3GYP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GYP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3gyp]] is a 1 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=3GYP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GYP FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 2.406&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3gyo|3gyo]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RTT106 ([http://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'>[https://proteopedia.org/fgij/fg.htm?mol=3gyp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gyp OCA], [https://pdbe.org/3gyp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gyp RCSB], [https://www.ebi.ac.uk/pdbsum/3gyp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gyp ProSAT]</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=3gyp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gyp OCA], [http://pdbe.org/3gyp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gyp RCSB], [http://www.ebi.ac.uk/pdbsum/3gyp PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gy/3gyp_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gy/3gyp_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
+[[Category: Large Structures]]
-[[Category: Huang, H]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Liu, Y]]
+[[Category: Huang H]]
-[[Category: Shi, Y]]
+[[Category: Liu Y]]
-[[Category: Teng, M]]
+[[Category: Shi Y]]
-[[Category: Chaperone]]
+[[Category: Teng M]]
-[[Category: Chromosomal protein]]
-[[Category: Histone chaperone]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-[[Category: Transposition]]

3gyp

From Proteopedia

Current revision

Rtt106p

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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