3mhh: Difference between revisions

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[[Image:3mhh.png|left|200px]]


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==Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module==
The line below this paragraph, containing "STRUCTURE_3mhh", creates the "Structure Box" on the page.
<StructureSection load='3mhh' size='340' side='right'caption='[[3mhh]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3mhh]] is a 4 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=3MHH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MHH FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.45&#8491;</td></tr>
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<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>
{{STRUCTURE_3mhh| PDB=3mhh |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3mhh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mhh OCA], [https://pdbe.org/3mhh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3mhh RCSB], [https://www.ebi.ac.uk/pdbsum/3mhh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3mhh ProSAT]</span></td></tr>
</table>
== Function ==
[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>
== 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/mh/3mhh_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <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/main_output.php?pdb_ID=3mhh ConSurf].
<div style="clear:both"></div>


===Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module===
==See Also==
 
*[[SAGA-associated factor|SAGA-associated factor]]
 
*[[Thioesterase 3D structures|Thioesterase 3D structures]]
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== References ==
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<references/>
(as it appears on PubMed at http://www.pubmed.gov), where 20395473 is the PubMed ID number.
__TOC__
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</StructureSection>
{{ABSTRACT_PUBMED_20395473}}
[[Category: Large Structures]]
 
==About this Structure==
[[3mhh]] 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=3MHH OCA].
 
==Reference==
<ref group="xtra">PMID:20395473</ref><references group="xtra"/>
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Ubiquitin thiolesterase]]
[[Category: Berndsen CE]]
[[Category: Berndsen, C E.]]
[[Category: Cohen RE]]
[[Category: Cohen, R E.]]
[[Category: Datta AB]]
[[Category: Datta, A B.]]
[[Category: Samara NL]]
[[Category: Samara, N L.]]
[[Category: Wolberger C]]
[[Category: Wolberger, C.]]
[[Category: Yao T]]
[[Category: Yao, T.]]
[[Category: Zhang X]]
[[Category: Zhang, X.]]
[[Category: Hydrolase-transcription complex]]
[[Category: Multi-protein complex]]

Latest revision as of 13:25, 21 February 2024

Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB moduleStructure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module

Structural highlights

3mhh is a 4 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 2.45Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ 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
  2. ↑ 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
  3. ↑ 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

3mhh, resolution 2.45Å

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