4w4u: Difference between revisions

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<StructureSection load='4w4u' size='340' side='right'caption='[[4w4u]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
<StructureSection load='4w4u' size='340' side='right'caption='[[4w4u]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4w4u]] 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=4W4U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4W4U FirstGlance]. <br>
<table><tr><td colspan='2'>[[4w4u]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_CEN.PK113-7D Saccharomyces cerevisiae CEN.PK113-7D] and [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=4W4U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4W4U 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>
</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 id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CENPK1137D_262 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=889517 Baker's yeast]), SUS1, CENPK1137D_4659 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=889517 Baker's yeast]), SGF11, CENPK1137D_1654 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=889517 Baker's yeast]), SGF73, YGL066W ([http://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=4w4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w4u OCA], [https://pdbe.org/4w4u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4w4u RCSB], [https://www.ebi.ac.uk/pdbsum/4w4u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4w4u ProSAT]</span></td></tr>
<tr id='activity'><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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4w4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w4u OCA], [http://pdbe.org/4w4u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4w4u RCSB], [http://www.ebi.ac.uk/pdbsum/4w4u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4w4u ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/SGF73_YEAST 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). [[http://www.uniprot.org/uniprot/N1NXA6_YEASC N1NXA6_YEASC]] Functions as component of the transcription regulatory histone acetylation (HAT) complex SAGA. 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 and promoter selectivity, interaction with transcription activators, and chromatin modification through histone acetylation and deubiquitination. SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). Involved in transcriptional regulation of a subset of SAGA-regulated genes. Within the SAGA complex, participates in a subcomplex, that specifically deubiquitinates histones H2B.[HAMAP-Rule:MF_03047][RuleBase:RU261113] [[http://www.uniprot.org/uniprot/N1P8F5_YEASC N1P8F5_YEASC]] Involved in mRNA export coupled transcription activation by association with both the TREX-2 and the SAGA complexes. 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 and promoter selectivity, interaction with transcription activators, and chromatin modification through histone acetylation and deubiquitination. Within the SAGA complex, participates to a subcomplex 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). TREX-2 participates in mRNA export and accurate chromatin positioning in the nucleus by tethering genes to the nuclear periphery. May also be involved in cytoplasmic mRNA decay by interaction with components of P-bodies.[HAMAP-Rule:MF_03046]  
[https://www.uniprot.org/uniprot/N1P0J5_YEASC N1P0J5_YEASC]  
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Baker's yeast]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Ubiquitinyl hydrolase 1]]
[[Category: Saccharomyces cerevisiae CEN PK113-7D]]
[[Category: Wolberger, C]]
[[Category: Saccharomyces cerevisiae S288C]]
[[Category: Yan, M]]
[[Category: Wolberger C]]
[[Category: Hydrolase-transcription complex]]
[[Category: Yan M]]
[[Category: Multi-protein complex]]
[[Category: Transcription-hydrolase complex]]

Revision as of 11:16, 29 March 2023

Structure of yeast SAGA DUBm with Sgf73 Y57A mutant at 2.8 angstroms resolutionStructure of yeast SAGA DUBm with Sgf73 Y57A mutant at 2.8 angstroms resolution

Structural highlights

4w4u is a 8 chain structure with sequence from Saccharomyces cerevisiae CEN.PK113-7D and Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

N1P0J5_YEASC

Publication Abstract from PubMed

The SAGA (Spt-Ada-Gcn5 acetyltransferase) complex performs multiple functions in transcription activation including deubiquitinating histone H2B, which is mediated by a subcomplex called the deubiquitinating module (DUBm). The yeast DUBm comprises a catalytic subunit, Ubp8, and three additional subunits, Sgf11, Sus1 and Sgf73, all of which are required for DUBm activity. A portion of the non-globular Sgf73 subunit lies between the Ubp8 catalytic domain and the ZnF-UBP domain and has been proposed to contribute to deubiquitinating activity by maintaining the catalytic domain in an active conformation. We report structural and solution studies of the DUBm containing two different Sgf73 point mutations that disrupt deubiquitinating activity. We find that the Sgf73 mutations abrogate deubiquitinating activity by impacting the Ubp8 ubiquitin-binding fingers region and they have an unexpected effect on the overall folding and stability of the DUBm complex. Taken together, our data suggest a role for Sgf73 in maintaining both the organization and the ubiquitin-binding conformation of Ubp8, thereby contributing to overall DUBm activity.

Uncovering the role of Sgf73 in maintaining SAGA deubiquitinating module structure and activity.,Yan M, Wolberger C J Mol Biol. 2015 Apr 24;427(8):1765-78. doi: 10.1016/j.jmb.2014.12.004. Epub 2014, Dec 17. PMID:25526805[1]

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

See Also

References

  1. ↑ Yan M, Wolberger C. Uncovering the role of Sgf73 in maintaining SAGA deubiquitinating module structure and activity. J Mol Biol. 2015 Apr 24;427(8):1765-78. doi: 10.1016/j.jmb.2014.12.004. Epub 2014, Dec 17. PMID:25526805 doi:http://dx.doi.org/10.1016/j.jmb.2014.12.004

4w4u, resolution 2.80Å

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