1zc1

From Proteopedia

(Difference between revisions)

Current revision

Ufd1 exhibits the AAA-ATPase fold with two distinct ubiquitin interaction sites

Structural highlights

1zc1 is a 1 chain structure with sequence from Saccharomyces cerevisiae. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

UFD1_YEAST Functions at a post-ubiquitation step in the ubiquitin fusion degradation (UFD) pathway. Has a role in the endoplasmic reticulum-associated degradation (ERAD) pathway. Required for the proteasome-dependent processing/activation of MGA2 and SPT23 transcription factors leading to the subsequent expression of OLE1. Has an additional role in the turnover of OLE1 where it targets ubiquitinated OLE1 and other proteins to the ERAD.^[1] ^[2] ^[3] ^[4]

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

Ufd1 mediates ubiquitin fusion degradation by association with Npl4 and Cdc48/p97. The Ufd1-ubiquitin interaction is essential for transfer of substrates to the proteasome. However, the mechanism and specificity of ubiquitin recognition by Ufd1 are poorly understood due to the lack of detailed structural information. Here, we present the solution structure of yeast Ufd1 N domain and show that it has two distinct binding sites for mono- and polyubiquitin. The structure exhibits striking similarities to the Cdc48/p97 N domain. It contains the double-psi beta barrel motif, which is thus identified as a ubiquitin binding domain. Significantly, Ufd1 shows higher affinity toward polyubiquitin than monoubiquitin, attributable to the utilization of separate binding sites with different affinities. Further studies revealed that the Ufd1-ubiquitin interaction involves hydrophobic contacts similar to those in well-characterized ubiquitin binding proteins. Our results provide a structural basis for a previously proposed synergistic binding of polyubiquitin by Cdc48/p97 and Ufd1.

Ufd1 exhibits the AAA-ATPase fold with two distinct ubiquitin interaction sites.,Park S, Isaacson R, Kim HT, Silver PA, Wagner G Structure. 2005 Jul;13(7):995-1005. PMID:16004872^[5]

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

References

↑ Rape M, Hoppe T, Gorr I, Kalocay M, Richly H, Jentsch S. Mobilization of processed, membrane-tethered SPT23 transcription factor by CDC48(UFD1/NPL4), a ubiquitin-selective chaperone. Cell. 2001 Nov 30;107(5):667-77. PMID:11733065
↑ Ye Y, Meyer HH, Rapoport TA. The AAA ATPase Cdc48/p97 and its partners transport proteins from the ER into the cytosol. Nature. 2001 Dec 6;414(6864):652-6. PMID:11740563 doi:http://dx.doi.org/10.1038/414652a
↑ Braun S, Matuschewski K, Rape M, Thoms S, Jentsch S. Role of the ubiquitin-selective CDC48(UFD1/NPL4 )chaperone (segregase) in ERAD of OLE1 and other substrates. EMBO J. 2002 Feb 15;21(4):615-21. PMID:11847109
↑ Park S, Isaacson R, Kim HT, Silver PA, Wagner G. Ufd1 exhibits the AAA-ATPase fold with two distinct ubiquitin interaction sites. Structure. 2005 Jul;13(7):995-1005. PMID:16004872 doi:10.1016/j.str.2005.04.013
↑ Park S, Isaacson R, Kim HT, Silver PA, Wagner G. Ufd1 exhibits the AAA-ATPase fold with two distinct ubiquitin interaction sites. Structure. 2005 Jul;13(7):995-1005. PMID:16004872 doi:10.1016/j.str.2005.04.013

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1zc1"

@@ Line 1: / Line 1: @@
 ==Ufd1 exhibits the AAA-ATPase fold with two distinct ubiquitin interaction sites==
-<StructureSection load='1zc1' size='340' side='right' caption='[[1zc1]], [[NMR_Ensembles_of_Models | 15 NMR models]]' scene=''>
+<StructureSection load='1zc1' size='340' side='right'caption='[[1zc1]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1zc1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZC1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1zc1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZC1 FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UFD1, PIP3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1zc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zc1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1zc1 RCSB], [http://www.ebi.ac.uk/pdbsum/1zc1 PDBsum]</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=1zc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zc1 OCA], [https://pdbe.org/1zc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zc1 RCSB], [https://www.ebi.ac.uk/pdbsum/1zc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zc1 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/UFD1_YEAST UFD1_YEAST]] Functions at a post-ubiquitation step in the ubiquitin fusion degradation (UFD) pathway. Has a role in the endoplasmic reticulum-associated degradation (ERAD) pathway. Required for the proteasome-dependent processing/activation of MGA2 and SPT23 transcription factors leading to the subsequent expression of OLE1. Has an additional role in the turnover of OLE1 where it targets ubiquitinated OLE1 and other proteins to the ERAD.<ref>PMID:11733065</ref> <ref>PMID:11740563</ref> <ref>PMID:11847109</ref> <ref>PMID:16004872</ref>
+[https://www.uniprot.org/uniprot/UFD1_YEAST UFD1_YEAST] Functions at a post-ubiquitation step in the ubiquitin fusion degradation (UFD) pathway. Has a role in the endoplasmic reticulum-associated degradation (ERAD) pathway. Required for the proteasome-dependent processing/activation of MGA2 and SPT23 transcription factors leading to the subsequent expression of OLE1. Has an additional role in the turnover of OLE1 where it targets ubiquitinated OLE1 and other proteins to the ERAD.<ref>PMID:11733065</ref> <ref>PMID:11740563</ref> <ref>PMID:11847109</ref> <ref>PMID:16004872</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/zc/1zc1_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zc/1zc1_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1zc1 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1zc1" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Isaacson, R]]
+[[Category: Isaacson R]]
-[[Category: Kim, H T]]
+[[Category: Kim HT]]
-[[Category: Park, S]]
+[[Category: Park S]]
-[[Category: Silver, P A]]
+[[Category: Silver PA]]
-[[Category: Wagner, G]]
+[[Category: Wagner G]]
-[[Category: Double-psi-beta-barrel]]
-[[Category: Protein turnover]]
-[[Category: Ufd1]]

1zc1

From Proteopedia

Current revision

Ufd1 exhibits the AAA-ATPase fold with two distinct ubiquitin interaction sites

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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