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 3: / Line 3: @@
 <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/Atcc_18824 Atcc 18824]. 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>
+<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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1zx2|1zx2]]</div></td></tr>
+</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BRE5 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), UBP3 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ubiquitin_thiolesterase Ubiquitin thiolesterase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.2.15 3.1.2.15] </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=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>  [[https://www.uniprot.org/uniprot/UBP3_YEAST UBP3_YEAST]] Has an ATP-independent isopeptidase activity, cleaving at the C-terminus of the ubiquitin moiety in natural or engineered linear fusion proteins, irrespective of their size or the presence of an N-terminal extension to ubiquitin. Plays a role in regulation of silencing by interacting with SIR4. Also, in conjunction with BRE5, cleaves ubiquitin, leading to the subsequent mono-ubiquitination of SEC23.<ref>PMID:12778054</ref> <ref>PMID:17632125</ref>
+[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]]
@@ Line 37: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: Ubiquitin thiolesterase]]
+[[Category: Saccharomyces cerevisiae]]
-[[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]]

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

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