3l3f: Difference between revisions

Latest revision as of 09:22, 30 October 2024

Crystal structure of a PFU-PUL domain pair of Saccharomyces cerevisiae Doa1/Ufd3

Structural highlights

3l3f is a 1 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 1.9Å
Ligands:	MSE
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DOA1_YEAST Participates in the regulation of the ubiquitin conjugation pathway involving CDC48 by hindering multiubiquitination of substrates at the CDC48 chaperone. May act by preventing the interaction between CDC48 and the E4 enzyme UFD2, leading to prevent multiubiquitination of substrates and subsequent degradation. Essential for maintaining cellular ubiquitin levels.^[1] ^[2]

Publication Abstract from PubMed

Doa1/Ufd3 is involved in ubiquitin (Ub)-dependent cellular processes in Saccharomyces cerevisiae, and consists of WD40, PFU, and PUL domains. Previous studies showed that the PFU and PUL domains interact with Ub and Hse1, and Cdc48, respectively. However, their detailed functional interactions with Doa1 remained elusive. We report the crystal structure of the PFU-PUL domain pair of yeast Doa1 at 1.9 A resolution. The conserved surface of the PFU domain may be involved in binding to Ub and Hse1. Unexpectedly, the PUL domain consists of an Armadillo (ARM)-like repeat structure. The positively charged concave surface of the PUL domain may bind to the negatively charged C-terminal region of Cdc48. A structural comparison of Doa1 with Ufd2 revealed that they share a similar ARM-like repeat, supporting a model in which Doa1 and Ufd2 compete for Cdc48 binding and may dictate the fate of ubiquitinated proteins in the proteasome pathway.

Crystal Structure of a PFU-PUL Domain Pair of Saccharomyces Cerevisiae Doa1/Ufd3.,Nishimasu R, Komori H, Higuchi Y, Nishimasu H, Hiroaki H Kobe J Med Sci. 2010 Oct 21;56(3):E125-39. PMID:21063153^[3]

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

References

↑ Russell NS, Wilkinson KD. Identification of a novel 29-linked polyubiquitin binding protein, Ufd3, using polyubiquitin chain analogues. Biochemistry. 2004 Apr 27;43(16):4844-54. PMID:15096053 doi:10.1021/bi035626r
↑ Ghislain M, Dohmen RJ, Levy F, Varshavsky A. Cdc48p interacts with Ufd3p, a WD repeat protein required for ubiquitin-mediated proteolysis in Saccharomyces cerevisiae. EMBO J. 1996 Sep 16;15(18):4884-99. PMID:8890162
↑ Nishimasu R, Komori H, Higuchi Y, Nishimasu H, Hiroaki H. Crystal Structure of a PFU-PUL Domain Pair of Saccharomyces Cerevisiae Doa1/Ufd3. Kobe J Med Sci. 2010 Oct 21;56(3):E125-39. PMID:21063153

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OCA

[1] Russell NS, Wilkinson KD. Identification of a novel 29-linked polyubiquitin binding protein, Ufd3, using polyubiquitin chain analogues. Biochemistry. 2004 Apr 27;43(16):4844-54. PMID:15096053 doi:10.1021/bi035626r

[2] Ghislain M, Dohmen RJ, Levy F, Varshavsky A. Cdc48p interacts with Ufd3p, a WD repeat protein required for ubiquitin-mediated proteolysis in Saccharomyces cerevisiae. EMBO J. 1996 Sep 16;15(18):4884-99. PMID:8890162

[3] Nishimasu R, Komori H, Higuchi Y, Nishimasu H, Hiroaki H. Crystal Structure of a PFU-PUL Domain Pair of Saccharomyces Cerevisiae Doa1/Ufd3. Kobe J Med Sci. 2010 Oct 21;56(3):E125-39. PMID:21063153

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='3l3f' size='340' side='right'caption='[[3l3f]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3l3f]] is a 1 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=3L3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3L3F FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3l3f]] is a 1 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=3L3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3L3F FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=3l3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l3f OCA], [https://pdbe.org/3l3f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3l3f RCSB], [https://www.ebi.ac.uk/pdbsum/3l3f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3l3f ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/DOA1_YEAST DOA1_YEAST]] Participates in the regulation of the ubiquitin conjugation pathway involving CDC48 by hindering multiubiquitination of substrates at the CDC48 chaperone. May act by preventing the interaction between CDC48 and the E4 enzyme UFD2, leading to prevent multiubiquitination of substrates and subsequent degradation. Essential for maintaining cellular ubiquitin levels.<ref>PMID:15096053</ref> <ref>PMID:8890162</ref>
+[https://www.uniprot.org/uniprot/DOA1_YEAST DOA1_YEAST] Participates in the regulation of the ubiquitin conjugation pathway involving CDC48 by hindering multiubiquitination of substrates at the CDC48 chaperone. May act by preventing the interaction between CDC48 and the E4 enzyme UFD2, leading to prevent multiubiquitination of substrates and subsequent degradation. Essential for maintaining cellular ubiquitin levels.<ref>PMID:15096053</ref> <ref>PMID:8890162</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: Higuchi, Y]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Komori, H]]
+[[Category: Higuchi Y]]
-[[Category: Kuno, T]]
+[[Category: Komori H]]
-[[Category: Nishimasu, R]]
+[[Category: Kuno T]]
-[[Category: Armadillo-like repeat structure]]
+[[Category: Nishimasu R]]
-[[Category: Nucleus]]
-[[Category: Protein binding]]
-[[Category: Ubl conjugation pathway]]

3l3f: Difference between revisions

Latest revision as of 09:22, 30 October 2024

Crystal structure of a PFU-PUL domain pair of Saccharomyces cerevisiae Doa1/Ufd3

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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