4fip

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:26, 14 March 2024) (edit) (undo)
 
(3 intermediate revisions not shown.)
Line 1: Line 1:
 +
==Structure of the SAGA Ubp8(S144N)/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module==
==Structure of the SAGA Ubp8(S144N)/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module==
-
<StructureSection load='4fip' size='340' side='right' caption='[[4fip]], [[Resolution|resolution]] 2.69&Aring;' scene=''>
+
<StructureSection load='4fip' size='340' side='right'caption='[[4fip]], [[Resolution|resolution]] 2.69&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4fip]] is a 8 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=4FIP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FIP FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4fip]] is a 8 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=4FIP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FIP FirstGlance]. <br>
-
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.686&#8491;</td></tr>
-
<tr><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]), SUS1, YBR111W-A ([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]), SGF73, YGL066W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitinyl_hydrolase_1 Ubiquitinyl hydrolase 1], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.19.12 3.4.19.12] </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=4fip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fip OCA], [https://pdbe.org/4fip PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fip RCSB], [https://www.ebi.ac.uk/pdbsum/4fip PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fip ProSAT]</span></td></tr>
-
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4fip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fip OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fip RCSB], [http://www.ebi.ac.uk/pdbsum/4fip PDBsum]</span></td></tr>
+
</table>
-
<table>
+
== Function ==
-
<div style="background-color:#fffaf0;">
+
[https://www.uniprot.org/uniprot/UBP8_YEAST 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.<ref>PMID:10026213</ref> <ref>PMID:14660634</ref> <ref>PMID:15657441</ref>
-
== Publication Abstract from PubMed ==
+
-
The deubiquitinating module (DUBm) of the SAGA coactivator contains the Ubp8 isopeptidase, Sgf11, Sus1, and Sgf73, which form a highly interconnected complex. Although Ubp8 contains a canonical USP catalytic domain, it is only active when in complex with the other DUBm subunits. The Sgf11 zinc finger (Sgf11-ZnF) binds near the Ubp8 active site and is essential for full activity, suggesting that the Sgf11-ZnF helps maintain the active conformation of Ubp8. We report structural and solution studies showing that deletion of the Sgf11-ZnF destabilizes incorporation of Ubp8 within the DUBm, giving rise to domain swapping with a second complex and misaligning active site residues. Activating mutations in Ubp8 that partially restore activity in the absence of the Sgf11-ZnF promote the monomeric form of the DUBm. Our data suggest an unexpected role for Sgf11 in compensating for the absence of structural features that maintain the active conformation of Ubp8.
+
-
 
+
-
A Role for Intersubunit Interactions in Maintaining SAGA Deubiquitinating Module Structure and Activity.,Samara NL, Ringel AE, Wolberger C Structure. 2012 Jul 3. PMID:22771212<ref>PMID:22771212</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
==See Also==
==See Also==
*[[SAGA-associated factor|SAGA-associated factor]]
*[[SAGA-associated factor|SAGA-associated factor]]
-
*[[Thioesterase|Thioesterase]]
+
*[[Thioesterase 3D structures|Thioesterase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Saccharomyces cerevisiae]]
+
[[Category: Large Structures]]
-
[[Category: Ubiquitinyl hydrolase 1]]
+
[[Category: Saccharomyces cerevisiae S288C]]
-
[[Category: Ringel, A E.]]
+
[[Category: Ringel AE]]
-
[[Category: Samara, N L.]]
+
[[Category: Samara NL]]
-
[[Category: Wolberger, C.]]
+
[[Category: Wolberger C]]
-
[[Category: Deubiquitination]]
+
-
[[Category: Domain-swapping]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Nucleosome]]
+
-
[[Category: Transcription]]
+

Current revision

Structure of the SAGA Ubp8(S144N)/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module

PDB ID 4fip

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4fip"
Personal tools