OCA at 19:39, 29 May 2024

2024-05-29T19:39:28Z

←Older revision		Revision as of 19:39, 29 May 2024
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-	====	+	==Structure of yeast Ubr1 in complex with Ubc2 and N-degron==
-	<StructureSection load='7mex' size='340' side='right'caption='[[7mex]]' scene=''>	+	<StructureSection load='7mex' size='340' side='right'caption='[[7mex]], [[Resolution\|resolution]] 3.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7mex]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MEX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MEX FirstGlance]. <br>
-	</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=7mex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mex OCA], [https://pdbe.org/7mex PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mex RCSB], [https://www.ebi.ac.uk/pdbsum/7mex PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mex ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.35Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7mex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mex OCA], [https://pdbe.org/7mex PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mex RCSB], [https://www.ebi.ac.uk/pdbsum/7mex PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mex ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/UBC_HUMAN UBC_HUMAN] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The N-degron pathway targets proteins that bear a destabilizing residue at the N terminus for proteasome-dependent degradation(1). In yeast, Ubr1-a single-subunit E3 ligase-is responsible for the Arg/N-degron pathway(2). How Ubr1 mediates the initiation of ubiquitination and the elongation of the ubiquitin chain in a linkage-specific manner through a single E2 ubiquitin-conjugating enzyme (Ubc2) remains unknown. Here we developed chemical strategies to mimic the reaction intermediates of the first and second ubiquitin transfer steps, and determined the cryo-electron microscopy structures of Ubr1 in complex with Ubc2, ubiquitin and two N-degron peptides, representing the initiation and elongation steps of ubiquitination. Key structural elements, including a Ubc2-binding region and an acceptor ubiquitin-binding loop on Ubr1, were identified and characterized. These structures provide mechanistic insights into the initiation and elongation of ubiquitination catalysed by Ubr1.
		+
		+	Structural insights into Ubr1-mediated N-degron polyubiquitination.,Pan M, Zheng Q, Wang T, Liang L, Mao J, Zuo C, Ding R, Ai H, Xie Y, Si D, Yu Y, Liu L, Zhao M Nature. 2021 Dec;600(7888):334-338. doi: 10.1038/s41586-021-04097-8. Epub 2021 , Nov 17. PMID:34789879<ref>PMID:34789879</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7mex" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ubiquitin protein ligase 3D structures\|Ubiquitin protein ligase 3D structures]]
		+	*[[3D structures of ubiquitin\|3D structures of ubiquitin]]
		+	*[[3D structures of ubiquitin conjugating enzyme\|3D structures of ubiquitin conjugating enzyme]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
		+	[[Category: Liang L]]
		+	[[Category: Liu L]]
		+	[[Category: Pan M]]
		+	[[Category: Wang T]]
		+	[[Category: Yu Y]]
		+	[[Category: Zhao M]]
		+	[[Category: Zheng Q]]

OCA at 12:36, 24 November 2021

2021-11-24T12:36:17Z

←Older revision		Revision as of 12:36, 24 November 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7mex ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7mex' size='340' side='right'caption='[[7mex]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~:	+	</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=7mex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mex OCA], [https://pdbe.org/7mex PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mex RCSB], [https://www.ebi.ac.uk/pdbsum/7mex PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mex ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 12:30, 27 October 2021

2021-10-27T12:30:38Z

←Older revision		Revision as of 12:30, 27 October 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7mex is ON HOLD	+	The entry 7mex is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 04:02, 6 October 2021

2021-10-06T04:02:52Z

←Older revision		Revision as of 04:02, 6 October 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7mex is ON HOLD ~~until Paper Publication~~	+	The entry 7mex is ON HOLD

	Authors:		Authors:

OCA at 06:18, 21 April 2021

2021-04-21T06:18:58Z

←Older revision		Revision as of 06:18, 21 April 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7mex is ON HOLD	+	The entry 7mex is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7mex" [edit=sysop:move=sysop]

2021-04-14T05:44:45Z

Protected "7mex" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:44, 14 April 2021

OCA: New page: '''Unreleased structure''' The entry 7mex is ON HOLD Authors: Description: Category: Unreleased Structures

2021-04-14T05:44:44Z

New page: '''Unreleased structure''' The entry 7mex is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7mex is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]