5k9p - Revision history

OCA at 10:43, 27 September 2023

OCA — Wed, 27 Sep 2023 10:43:46 GMT

←Older revision		Revision as of 10:43, 27 September 2023
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	<StructureSection load='5k9p' size='340' side='right'caption='[[5k9p]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='5k9p' size='340' side='right'caption='[[5k9p]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k9p]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K9P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5K9P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k9p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K9P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K9P FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non~~-~~Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</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]] 1.55Å</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=5k9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k9p OCA], [~~http~~://pdbe.org/5k9p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5k9p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5k9p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5k9p ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</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=5k9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k9p OCA], [https://pdbe.org/5k9p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k9p RCSB], [https://www.ebi.ac.uk/pdbsum/5k9p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k9p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/UBB_HUMAN UBB_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/UBB_HUMAN UBB_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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[~~Ubiquitin~~\|~~Ubiquitin~~]]	+	*[[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: Chin~~, J W~~]]	+	[[Category: Chin JW]]
-	[[Category: Huguenin-Dezot, N]]	+	[[Category: Huguenin-Dezot N]]
-	~~[[Category: Cell cycle]]~~	+
-	~~[[Category: Phospho-ubiquitin]]~~	+
-	~~[[Category: Phosphoubiquitin]]~~	+
-	~~[[Category: Signaling protein]]~~	+
-	~~[[Category: Ubiquitin~~]]	+

OCA at 09:28, 1 July 2020

OCA — Wed, 01 Jul 2020 09:28:50 GMT

←Older revision		Revision as of 09:28, 1 July 2020
Line 1:		Line 1:

	==Ser20 phosphorylated ubiquitin==		==Ser20 phosphorylated ubiquitin==
-	<StructureSection load='5k9p' size='340' side='right' caption='[[5k9p]], [[Resolution\|resolution]] 1.55Å' scene=''>	+	<StructureSection load='5k9p' size='340' side='right'caption='[[5k9p]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k9p]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K9P OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5K9P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k9p]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K9P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5K9P FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</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=5k9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k9p OCA], [http://pdbe.org/5k9p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k9p RCSB], [http://www.ebi.ac.uk/pdbsum/5k9p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k9p 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=5k9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k9p OCA], [http://pdbe.org/5k9p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k9p RCSB], [http://www.ebi.ac.uk/pdbsum/5k9p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k9p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 25:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Chin, J W]]		[[Category: Chin, J W]]
	[[Category: Huguenin-Dezot, N]]		[[Category: Huguenin-Dezot, N]]

OCA at 10:29, 13 September 2017

OCA — Wed, 13 Sep 2017 10:29:27 GMT

←Older revision		Revision as of 10:29, 13 September 2017
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5k9p" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5k9p" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ubiquitin\|Ubiquitin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:32, 3 August 2016

OCA — Wed, 03 Aug 2016 20:32:40 GMT

←Older revision		Revision as of 20:32, 3 August 2016
Line 9:		Line 9:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/UBB_HUMAN UBB_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>		[[http://www.uniprot.org/uniprot/UBB_HUMAN UBB_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 ==
		+	Ubiquitin is post-translationally modified by phosphorylation at several sites, but the consequences of these modifications are largely unknown. Here, we synthesize multi-milligram quantities of ubiquitin phosphorylated at serine 20, serine 57, and serine 65 via genetic code expansion. We use these phosphoubiquitins for the enzymatic assembly of 20 isomeric phosphoubiquitin dimers, with different sites of isopeptide linkage and/or phosphorylation. We discover that phosphorylation of serine 20 on ubiquitin converts UBE3C from a dual-specificity E3 ligase into a ligase that primarily synthesizes K48 chains. We profile the activity of 31 deubiquitinases on the isomeric phosphoubiquitin dimers in 837 reactions, and we discover that phosphorylation at distinct sites in ubiquitin can activate or repress cleavage of a particular linkage by deubiquitinases and that phosphorylation at a single site in ubiquitin can control the specificity of deubiquitinases for distinct ubiquitin linkages.
		+
		+	Synthesis of Isomeric Phosphoubiquitin Chains Reveals that Phosphorylation Controls Deubiquitinase Activity and Specificity.,Huguenin-Dezot N, De Cesare V, Peltier J, Knebel A, Kristaryianto YA, Rogerson DT, Kulathu Y, Trost M, Chin JW Cell Rep. 2016 Jul 26;16(4):1180-93. doi: 10.1016/j.celrep.2016.06.064. Epub 2016, Jul 14. PMID:27425610<ref>PMID:27425610</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5k9p" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:38, 26 July 2016

OCA — Tue, 26 Jul 2016 15:38:20 GMT

←Older revision		Revision as of 15:38, 26 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5k9p is ~~ON HOLD~~ ~~until Paper Publication~~	+	==Ser20 phosphorylated ubiquitin==
-		+	<StructureSection load='5k9p' size='340' side='right' caption='[[5k9p]], [[Resolution\|resolution]] 1.55Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5k9p]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K9P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K9P FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5k9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k9p OCA], [http://pdbe.org/5k9p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k9p RCSB], [http://www.ebi.ac.uk/pdbsum/5k9p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k9p ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/UBB_HUMAN UBB_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>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chin, J W]]
		+	[[Category: Huguenin-Dezot, N]]
		+	[[Category: Cell cycle]]
		+	[[Category: Phospho-ubiquitin]]
		+	[[Category: Phosphoubiquitin]]
		+	[[Category: Signaling protein]]
		+	[[Category: Ubiquitin]]

OCA at 00:09, 13 July 2016

OCA — Wed, 13 Jul 2016 00:09:09 GMT

←Older revision		Revision as of 00:09, 13 July 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5k9p is ON HOLD	+	The entry 5k9p is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5k9p" [edit=sysop:move=sysop]

OCA — Mon, 20 Jun 2016 13:36:31 GMT

Protected "5k9p" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:36, 20 June 2016

OCA: New page: '''Unreleased structure''' The entry 5k9p is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Mon, 20 Jun 2016 13:36:30 GMT

New page: '''Unreleased structure''' The entry 5k9p is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5k9p is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]