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New page: left|200px<br /><applet load="2qiy" size="350" color="white" frame="true" align="right" spinBox="true" caption="2qiy, resolution 1.69Å" /> '''yeast Deubiquitinase...
 
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[[Image:2qiy.gif|left|200px]]<br /><applet load="2qiy" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2qiy, resolution 1.69&Aring;" />
'''yeast Deubiquitinase Ubp3 and Bre5 cofactor complex'''<br />


==Overview==
==yeast Deubiquitinase Ubp3 and Bre5 cofactor complex==
Yeast Ubp3 and its co-factor Bre5 form a deubiquitylation complex to, regulate protein transport between the endoplasmic reticulum and Golgi, compartments of the cell. A novel N-terminal domain of the Ubp3 catalytic, subunit forms a complex with the NTF2-like domain of the Bre5 regulatory, subunit. Here, we report the X-ray crystal structure of an Ubp3-Bre5, complex and show that it forms a symmetric hetero-tetrameric complex in, which the Bre5 NTF2-like domain dimer interacts with two L-shaped, beta-strand-turn-alpha-helix motifs of Ubp3. The Ubp3 N-terminal domain, binds within a hydrophobic cavity on the surface of the Bre5 NTF2-like, domain subunit with conserved residues within both proteins interacting, predominantly through antiparallel beta-sheet hydrogen bonds and van der, Waals contacts. Structure-based mutagenesis and functional studies confirm, the significance of the observed interactions for Ubp3-Bre5 association in, vitro and Ubp3 function in vivo. Comparison of the structure to other, protein complexes with NTF2-like domains shows that the Ubp3-Bre5, interface is novel. Together, these studies provide new insights into Ubp3, recognition by Bre5 and into protein recognition by NTF2-like domains.
<StructureSection load='2qiy' size='340' side='right'caption='[[2qiy]], [[Resolution|resolution]] 1.69&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2qiy]] 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=2QIY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QIY FirstGlance]. <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]] 1.69&#8491;</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=2qiy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qiy OCA], [https://pdbe.org/2qiy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qiy RCSB], [https://www.ebi.ac.uk/pdbsum/2qiy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qiy ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/BRE5_YEAST BRE5_YEAST] Has a role in de-ubiquitination. In conjunction with UBP3, cleaves ubiquitin, leading to the subsequent mono-ubiquitination of sec23.<ref>PMID:12778054</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/qi/2qiy_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=2qiy ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Yeast Ubp3 and its co-factor Bre5 form a deubiquitylation complex to regulate protein transport between the endoplasmic reticulum and Golgi compartments of the cell. A novel N-terminal domain of the Ubp3 catalytic subunit forms a complex with the NTF2-like domain of the Bre5 regulatory subunit. Here, we report the X-ray crystal structure of an Ubp3-Bre5 complex and show that it forms a symmetric hetero-tetrameric complex in which the Bre5 NTF2-like domain dimer interacts with two L-shaped beta-strand-turn-alpha-helix motifs of Ubp3. The Ubp3 N-terminal domain binds within a hydrophobic cavity on the surface of the Bre5 NTF2-like domain subunit with conserved residues within both proteins interacting predominantly through antiparallel beta-sheet hydrogen bonds and van der Waals contacts. Structure-based mutagenesis and functional studies confirm the significance of the observed interactions for Ubp3-Bre5 association in vitro and Ubp3 function in vivo. Comparison of the structure to other protein complexes with NTF2-like domains shows that the Ubp3-Bre5 interface is novel. Together, these studies provide new insights into Ubp3 recognition by Bre5 and into protein recognition by NTF2-like domains.


==About this Structure==
Molecular basis for bre5 cofactor recognition by the ubp3 deubiquitylating enzyme.,Li K, Ossareh-Nazari B, Liu X, Dargemont C, Marmorstein R J Mol Biol. 2007 Sep 7;372(1):194-204. Epub 2007 Jun 27. PMID:17632125<ref>PMID:17632125</ref>
2QIY is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QIY OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Molecular basis for bre5 cofactor recognition by the ubp3 deubiquitylating enzyme., Li K, Ossareh-Nazari B, Liu X, Dargemont C, Marmorstein R, J Mol Biol. 2007 Sep 7;372(1):194-204. Epub 2007 Jun 27. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17632125 17632125]
</div>
[[Category: Protein complex]]
<div class="pdbe-citations 2qiy" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Thioesterase 3D structures|Thioesterase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Ubiquitin thiolesterase]]
[[Category: Li K]]
[[Category: Li, K.]]
[[Category: Liu X]]
[[Category: Liu, X.]]
[[Category: Marmorstein R]]
[[Category: Marmorstein, R.]]
[[Category: deubiquitylation]]
[[Category: hydrolase]]
[[Category: ntf2]]
[[Category: phosphorylation]]
[[Category: protein-protein recognition]]
[[Category: rna-binding ]]
[[Category: signaling protein/hydrolase complex]]
[[Category: thiol protease]]
[[Category: ubiquitin-specific processing proteases(ubps)]]
[[Category: ubl conjugation pathway]]
 
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Retrieved from "https://proteopedia.org/2qiy"