5zq7 - Revision history

OCA at 09:03, 22 November 2023

OCA — Wed, 22 Nov 2023 09:03:35 GMT

←Older revision		Revision as of 09:03, 22 November 2023
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	<StructureSection load='5zq7' size='340' side='right'caption='[[5zq7]], [[Resolution\|resolution]] 2.85Å' scene=''>		<StructureSection load='5zq7' size='340' side='right'caption='[[5zq7]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zq7]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZQ7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5ZQ7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zq7]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Legionella_pneumophila Legionella pneumophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZQ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZQ7 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>~~, ~~<scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 2.847Å</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>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5zq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zq7 OCA], [~~http~~://pdbe.org/5zq7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zq7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zq7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zq7 ProSAT]</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=5zq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zq7 OCA], [https://pdbe.org/5zq7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zq7 RCSB], [https://www.ebi.ac.uk/pdbsum/5zq7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zq7 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://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>	+	[https://www.uniprot.org/uniprot/Q6BBR6_LEGPN Q6BBR6_LEGPN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5zq7" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5zq7" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[3D structures of ubiquitin\|3D structures of ubiquitin]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Gao, A~~]]	+	[[Category: Legionella pneumophila]]
-	[[Category: Gao~~, P~~]]	+	[[Category: Gao A]]
-	[[Category: ~~Wang, Y~~]]	+	[[Category: Gao P]]
-	[[Category: ~~Cell invasion]]~~	+	[[Category: Wang Y]]
-	~~[[Category: Ubiquitination~~]]	+

OCA at 21:23, 28 October 2020

OCA — Wed, 28 Oct 2020 21:23:40 GMT

←Older revision		Revision as of 21:23, 28 October 2020
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	==SidE-Ubi-NAD==		==SidE-Ubi-NAD==
-	<StructureSection load='5zq7' size='340' side='right' caption='[[5zq7]], [[Resolution\|resolution]] 2.85Å' scene=''>	+	<StructureSection load='5zq7' size='340' side='right'caption='[[5zq7]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zq7]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZQ7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zq7]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ZQ7 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></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>		<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>
-	<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=5zq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zq7 OCA], [http://pdbe.org/5zq7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zq7 RCSB], [http://www.ebi.ac.uk/pdbsum/5zq7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zq7 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5zq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zq7 OCA], [http://pdbe.org/5zq7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zq7 RCSB], [http://www.ebi.ac.uk/pdbsum/5zq7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zq7 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Gao, A]]		[[Category: Gao, A]]
	[[Category: Gao, P]]		[[Category: Gao, P]]

OCA at 07:19, 23 May 2018

OCA — Wed, 23 May 2018 07:19:46 GMT

←Older revision		Revision as of 07:19, 23 May 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zq7 is ~~ON HOLD~~ ~~until Apr 17 2020~~	+	==SidE-Ubi-NAD==
		+	<StructureSection load='5zq7' size='340' side='right' caption='[[5zq7]], [[Resolution\|resolution]] 2.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5zq7]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZQ7 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></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>
		+	<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=5zq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zq7 OCA], [http://pdbe.org/5zq7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zq7 RCSB], [http://www.ebi.ac.uk/pdbsum/5zq7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zq7 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://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 ==
		+	Ubiquitination constitutes one of the most important signaling mechanisms in eukaryotes. Conventional ubiquitination is catalyzed by the universally conserved E1-E2-E3 three-enzyme cascade in an ATP-dependent manner. The newly identified SidE family effectors of the pathogen Legionella pneumophila ubiquitinate several human proteins by a different mechanism without engaging any of the conventional ubiquitination machinery. We now report the crystal structures of SidE alone and in complex with ubiquitin, NAD, and ADP-ribose, thereby capturing different conformations of SidE before and after ubiquitin and ligand binding. The structures of ubiquitin bound to both mART and PDE domains reveal several unique features of the two reaction steps catalyzed by SidE. Further, the structural and biochemical results demonstrate that SidE family members do not recognize specific structural folds of the substrate proteins. Our studies provide both structural explanations for the functional observations and new insights into the molecular mechanisms of this non-canonical ubiquitination machinery.

-	~~Authors~~:	+	Structural Insights into Non-canonical Ubiquitination Catalyzed by SidE.,Wang Y, Shi M, Feng H, Zhu Y, Liu S, Gao A, Gao P Cell. 2018 May 17;173(5):1231-1243.e16. doi: 10.1016/j.cell.2018.04.023. Epub, 2018 May 3. PMID:29731171<ref>PMID:29731171</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5zq7" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Gao, A]]
		+	[[Category: Gao, P]]
		+	[[Category: Wang, Y]]
		+	[[Category: Cell invasion]]
		+	[[Category: Ubiquitination]]

OCA at 03:49, 16 May 2018

OCA — Wed, 16 May 2018 03:49:55 GMT

←Older revision		Revision as of 03:49, 16 May 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zq7 is ON HOLD	+	The entry 5zq7 is ON HOLD until Apr 17 2020

	Authors:		Authors:

OCA: Protected "5zq7" [edit=sysop:move=sysop]

OCA — Wed, 25 Apr 2018 03:54:37 GMT

Protected "5zq7" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:54, 25 April 2018

OCA: New page: '''Unreleased structure''' The entry 5zq7 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 25 Apr 2018 03:54:35 GMT

New page: '''Unreleased structure''' The entry 5zq7 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5zq7 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]