2qiy: Difference between revisions

Latest revision as of 11:33, 30 August 2023

yeast Deubiquitinase Ubp3 and Bre5 cofactor complex

Structural highlights

2qiy 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 1.69Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BRE5_YEAST Has a role in de-ubiquitination. In conjunction with UBP3, cleaves ubiquitin, leading to the subsequent mono-ubiquitination of sec23.^[1]

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

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.

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^[2]

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

References

↑ Cohen M, Stutz F, Belgareh N, Haguenauer-Tsapis R, Dargemont C. Ubp3 requires a cofactor, Bre5, to specifically de-ubiquitinate the COPII protein, Sec23. Nat Cell Biol. 2003 Jul;5(7):661-7. PMID:12778054 doi:https://dx.doi.org/10.1038/ncb1003
↑ Li K, Ossareh-Nazari B, Liu X, Dargemont C, Marmorstein R. Molecular basis for bre5 cofactor recognition by the ubp3 deubiquitylating enzyme. J Mol Biol. 2007 Sep 7;372(1):194-204. Epub 2007 Jun 27. PMID:17632125 doi:10.1016/j.jmb.2007.06.052

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Cohen M, Stutz F, Belgareh N, Haguenauer-Tsapis R, Dargemont C. Ubp3 requires a cofactor, Bre5, to specifically de-ubiquitinate the COPII protein, Sec23. Nat Cell Biol. 2003 Jul;5(7):661-7. PMID:12778054 doi:https://dx.doi.org/10.1038/ncb1003

[2] Li K, Ossareh-Nazari B, Liu X, Dargemont C, Marmorstein R. Molecular basis for bre5 cofactor recognition by the ubp3 deubiquitylating enzyme. J Mol Biol. 2007 Sep 7;372(1):194-204. Epub 2007 Jun 27. PMID:17632125 doi:10.1016/j.jmb.2007.06.052

[1]

[2]

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:2qiy.png|left|200px]]
-<!--
+==yeast Deubiquitinase Ubp3 and Bre5 cofactor complex==
-The line below this paragraph, containing "STRUCTURE_2qiy", creates the "Structure Box" on the page.
+<StructureSection load='2qiy' size='340' side='right'caption='[[2qiy]], [[Resolution|resolution]] 1.69&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'>[[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>
-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]] 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>
-{{STRUCTURE_2qiy|  PDB=2qiy  |  SCENE=  }}
+</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.
-===yeast Deubiquitinase Ubp3 and Bre5 cofactor complex===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2qiy" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17632125}}, adds the Publication Abstract to the page
+*[[Thioesterase 3D structures|Thioesterase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17632125 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17632125}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-QIY is a 4 chains structure of sequences 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=2QIY OCA].
-==Reference==
-<ref group="xtra">PMID:17632125</ref><ref group="xtra">PMID:15955808</ref><references group="xtra"/>
 [[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: Ubl conjugation pathway]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 11:00:57 2009''

2qiy: Difference between revisions

Latest revision as of 11:33, 30 August 2023

yeast Deubiquitinase Ubp3 and Bre5 cofactor complex

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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