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3m99

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Revision as of 05:19, 5 August 2016

Structure of the Ubp8-Sgf11-Sgf73-Sus1 SAGA DUB module

Structural highlights

3m99 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:	UBP8, YM9959.05, YMR223W (ATCC 18824), SGF11, YPL047W (ATCC 18824), SUS1, YBR111W-A (ATCC 18824), SGF73, SGF73 (AA 1-104), YGL066W (ATCC 18824)
Activity:	Ubiquitin thiolesterase, with EC number 3.1.2.15
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[SGF73_YEAST] Functions as component of the transcription regulatory histone acetylation (HAT) complex SAGA. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). [UBP8_YEAST] Functions as histone deubiquitinating component of the transcription regulatory histone acetylation (HAT) complexes SAGA and SLIK. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus. Together with SGF11, is required for histone H2B deubiquitination.^[1] ^[2] ^[3] [SUS1_YEAST] Involved in mRNA export coupled transcription activation by association with both the TREX-2 and the SAGA complexes. The transcription regulatory histone acetylation (HAT) complex SAGA is involved in RNA polymerase II-dependent regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SUS1 forms a distinct functional SAGA module with UBP8, SGF11 and SGF73 required for deubiquitination of H2B and for the maintenance of steady-state H3 methylation levels. The TREX-2 complex functions in docking export-competent ribonucleoprotein particles (mRNPs) to the nuclear entrance of the nuclear pore complex (nuclear basket), by association with components of the nuclear mRNA export machinery (MEX67-MTR2 and SUB2) in the nucleoplasm and the nucleoporin NUP1 at the nuclear basket. TREX-2 participates in mRNA export and accurate chromatin positioning in the nucleus by tethering genes to the nuclear periphery. SUS1 has also a role in mRNP biogenesis and maintenance of genome integrity through preventing RNA-mediated genome instability. Finally SUS1 has a role in response to DNA damage induced by methyl methane sulfonate (MMS) and replication arrest induced by hydroxyurea.^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] [SGF11_YEAST] Component of the transcription regulatory histone acetylation (HAT) complex SAGA. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SGF11 is involved in transcriptional regulation of a subset of SAGA-regulated genes. Within the SAGA complex, participates in a subcomplex with SUS1, SGF73 and UBP8 required for deubiquitination of H2B and for the maintenance of steady-state H3 methylation levels. It is required to recruit UBP8 and SUS1 into the SAGA complex.^[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

Deubiquitinating enzymes (DUBs) regulate diverse cellular functions by cleaving ubiquitin from specific protein substrates. How their activities are modulated in various cellular contexts remains poorly understood. The yeast deubiquitinase Ubp8 protein is recruited and activated by the SAGA complex and, together with Sgf11, Sus1, and Sgf73, forms a DUB module responsible for deubiquitinating histone H2B during gene expression. Here, we report the crystal structure of the complete SAGA DUB module, which features two functional lobes structurally coupled by Sgf73. In the "assembly lobe," a long Sgf11 N-terminal helix is clamped onto the Ubp8 ZnF-UBP domain by Sus1. In the "catalytic lobe," an Sgf11 C-terminal zinc-finger domain binds to the Ubp8 catalytic domain next to its active site. Our structural and functional analyses reveal a central role of Sgf11 and Sgf73 in activating Ubp8 for deubiquitinating histone H2B and demonstrate how a DUB can be allosterically regulated by its nonsubstrate partners.

Structural basis for assembly and activation of the heterotetrameric SAGA histone H2B deubiquitinase module.,Kohler A, Zimmerman E, Schneider M, Hurt E, Zheng N Cell. 2010 May 14;141(4):606-17. Epub 2010 Apr 29. PMID:20434206^[13]

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

References

↑ Grant PA, Eberharter A, John S, Cook RG, Turner BM, Workman JL. Expanded lysine acetylation specificity of Gcn5 in native complexes. J Biol Chem. 1999 Feb 26;274(9):5895-900. PMID:10026213
↑ Daniel JA, Torok MS, Sun ZW, Schieltz D, Allis CD, Yates JR 3rd, Grant PA. Deubiquitination of histone H2B by a yeast acetyltransferase complex regulates transcription. J Biol Chem. 2004 Jan 16;279(3):1867-71. Epub 2003 Dec 3. PMID:14660634 doi:10.1074/jbc.C300494200
↑ Ingvarsdottir K, Krogan NJ, Emre NC, Wyce A, Thompson NJ, Emili A, Hughes TR, Greenblatt JF, Berger SL. H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisiae SAGA complex. Mol Cell Biol. 2005 Feb;25(3):1162-72. PMID:15657441 doi:25/3/1162
↑ Fischer T, Rodriguez-Navarro S, Pereira G, Racz A, Schiebel E, Hurt E. Yeast centrin Cdc31 is linked to the nuclear mRNA export machinery. Nat Cell Biol. 2004 Sep;6(9):840-8. Epub 2004 Aug 15. PMID:15311284 doi:10.1038/ncb1163
↑ Kastenmayer JP, Ni L, Chu A, Kitchen LE, Au WC, Yang H, Carter CD, Wheeler D, Davis RW, Boeke JD, Snyder MA, Basrai MA. Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae. Genome Res. 2006 Mar;16(3):365-73. PMID:16510898 doi:16/3/365
↑ Kohler A, Pascual-Garcia P, Llopis A, Zapater M, Posas F, Hurt E, Rodriguez-Navarro S. The mRNA export factor Sus1 is involved in Spt/Ada/Gcn5 acetyltransferase-mediated H2B deubiquitinylation through its interaction with Ubp8 and Sgf11. Mol Biol Cell. 2006 Oct;17(10):4228-36. Epub 2006 Jul 19. PMID:16855026 doi:E06-02-0098
↑ Cabal GG, Genovesio A, Rodriguez-Navarro S, Zimmer C, Gadal O, Lesne A, Buc H, Feuerbach-Fournier F, Olivo-Marin JC, Hurt EC, Nehrbass U. SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope. Nature. 2006 Jun 8;441(7094):770-3. PMID:16760982 doi:10.1038/nature04752
↑ Pascual-Garcia P, Govind CK, Queralt E, Cuenca-Bono B, Llopis A, Chavez S, Hinnebusch AG, Rodriguez-Navarro S. Sus1 is recruited to coding regions and functions during transcription elongation in association with SAGA and TREX2. Genes Dev. 2008 Oct 15;22(20):2811-22. doi: 10.1101/gad.483308. PMID:18923079 doi:10.1101/gad.483308
↑ Gonzalez-Aguilera C, Tous C, Gomez-Gonzalez B, Huertas P, Luna R, Aguilera A. The THP1-SAC3-SUS1-CDC31 complex works in transcription elongation-mRNA export preventing RNA-mediated genome instability. Mol Biol Cell. 2008 Oct;19(10):4310-8. doi: 10.1091/mbc.E08-04-0355. Epub 2008, Jul 30. PMID:18667528 doi:10.1091/mbc.E08-04-0355
↑ Chekanova JA, Abruzzi KC, Rosbash M, Belostotsky DA. Sus1, Sac3, and Thp1 mediate post-transcriptional tethering of active genes to the nuclear rim as well as to non-nascent mRNP. RNA. 2008 Jan;14(1):66-77. Epub 2007 Nov 14. PMID:18003937 doi:10.1261/rna.764108
↑ Ingvarsdottir K, Krogan NJ, Emre NC, Wyce A, Thompson NJ, Emili A, Hughes TR, Greenblatt JF, Berger SL. H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisiae SAGA complex. Mol Cell Biol. 2005 Feb;25(3):1162-72. PMID:15657441 doi:25/3/1162
↑ Lee KK, Florens L, Swanson SK, Washburn MP, Workman JL. The deubiquitylation activity of Ubp8 is dependent upon Sgf11 and its association with the SAGA complex. Mol Cell Biol. 2005 Feb;25(3):1173-82. PMID:15657442 doi:http://dx.doi.org/10.1128/MCB.25.3.1173-1182.2005
↑ Kohler A, Zimmerman E, Schneider M, Hurt E, Zheng N. Structural basis for assembly and activation of the heterotetrameric SAGA histone H2B deubiquitinase module. Cell. 2010 May 14;141(4):606-17. Epub 2010 Apr 29. PMID:20434206 doi:10.1016/j.cell.2010.04.026

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3m99"

@@ Line 1: / Line 1: @@
 ==Structure of the Ubp8-Sgf11-Sgf73-Sus1 SAGA DUB module==
 <StructureSection load='3m99' size='340' side='right' caption='[[3m99]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3m99]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M99 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3M99 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3m99]] 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=3M99 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3M99 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UBP8, YM9959.05, YMR223W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), SGF11, YPL047W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), SUS1, YBR111W-A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), SGF73, SGF73 (AA 1-104), YGL066W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UBP8, YM9959.05, YMR223W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), SGF11, YPL047W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), SUS1, YBR111W-A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), SGF73, SGF73 (AA 1-104), YGL066W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitin_thiolesterase Ubiquitin thiolesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.2.15 3.1.2.15] </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=3m99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m99 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3m99 RCSB], [http://www.ebi.ac.uk/pdbsum/3m99 PDBsum]</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=3m99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m99 OCA], [http://pdbe.org/3m99 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3m99 RCSB], [http://www.ebi.ac.uk/pdbsum/3m99 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3m99 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 18: / Line 19: @@
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3m99 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 29: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3m99" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 36: / Line 38: @@
 __TOC__
 </StructureSection>
-[[Category: Saccharomyces cerevisiae]]
+[[Category: Atcc 18824]]
 [[Category: Ubiquitin thiolesterase]]
 [[Category: Hurt, E]]

3m99

From Proteopedia

Revision as of 05:19, 5 August 2016

Structure of the Ubp8-Sgf11-Sgf73-Sus1 SAGA DUB module

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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