1zc1

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:10, 15 May 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1zc1.gif|left|200px]]
 
-
{{Structure
+
==Ufd1 exhibits the AAA-ATPase fold with two distinct ubiquitin interaction sites==
-
|PDB= 1zc1 |SIZE=350|CAPTION= <scene name='initialview01'>1zc1</scene>
+
<StructureSection load='1zc1' size='340' side='right'caption='[[1zc1]]' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND=
+
<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>
-
|ACTIVITY=
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-
|GENE= UFD1, PIP3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])
+
<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>
-
|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG5140 UFD1], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam03152 UFD1]</span>
+
</table>
-
|RESOURCES=<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.ebi.ac.uk/pdbsum/1zc1 PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=1zc1 RCSB]</span>
+
== Function ==
-
}}
+
[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 ==
-
'''Ufd1 exhibits the AAA-ATPase fold with two distinct ubiquitin interaction sites'''
+
[[Image:Consurf_key_small.gif|200px|right]]
-
 
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==Overview==
+
<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/main_output.php?pdb_ID=1zc1 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== 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 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.
-
==About this Structure==
+
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<ref>PMID:16004872</ref>
-
1ZC1 is a [[Single protein]] structure of 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=1ZC1 OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
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:[http://www.ncbi.nlm.nih.gov/pubmed/16004872 16004872]
+
</div>
 +
<div class="pdbe-citations 1zc1" style="background-color:#fffaf0;"></div>
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
-
[[Category: Single protein]]
+
[[Category: Isaacson R]]
-
[[Category: Isaacson, R.]]
+
[[Category: Kim HT]]
-
[[Category: Kim, H T.]]
+
[[Category: Park S]]
-
[[Category: Park, S.]]
+
[[Category: Silver PA]]
-
[[Category: Silver, P A.]]
+
[[Category: Wagner G]]
-
[[Category: Wagner, G.]]
+
-
[[Category: double-psi-beta-barrel]]
+
-
[[Category: ufd1]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 26 06:17:56 2008''
+

Current revision

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

PDB ID 1zc1

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

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