5ulh - Revision history

OCA at 14:27, 6 March 2024

2024-03-06T14:27:59Z

←Older revision		Revision as of 14:27, 6 March 2024
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	==Structure of RNF165 in complex with a UbcH5b~Ub conjugate==		==Structure of RNF165 in complex with a UbcH5b~Ub conjugate==
-	<StructureSection load='5ulh' size='340' side='right' caption='[[5ulh]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='5ulh' size='340' side='right'caption='[[5ulh]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ulh]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ULH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ULH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ulh]] is a 3 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=5ULH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ULH FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.95Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ulf\|5ulf]]~~, [[~~5ulk~~\|~~5ulk~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9606 HUMAN]), UBB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN]), RNF165 ([http~~:~~//www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5ulh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ulh OCA], [https://pdbe.org/5ulh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ulh RCSB], [https://www.ebi.ac.uk/pdbsum/5ulh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ulh ProSAT]</span></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/RING-type_E3_ubiquitin_transferase RING-type E3 ubiquitin transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.27 2.3.2.27]~~ </~~span~~></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=5ulh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ulh OCA], [~~http~~://pdbe.org/5ulh PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ulh RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ulh PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ulh ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/UB2D2_HUMAN UB2D2_HUMAN]] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-48'-linked polyubiquitination. Mediates the selective degradation of short-lived and abnormal proteins. Functions in the E6/E6-AP-induced ubiquitination of p53/TP53. Mediates ubiquitination of PEX5 and autoubiquitination of STUB1 and TRAF6. Involved in the signal-induced conjugation and subsequent degradation of NFKBIA, FBXW2-mediated GCM1 ubiquitination and degradation, MDM2-dependent degradation of p53/TP53 and the activation of MAVS in the mitochondria by DDX58/RIG-I in response to viral infection. Essential for viral activation of IRF3.<ref>PMID:10329681</ref> <ref>PMID:15280377</ref> <ref>PMID:18042044</ref> <ref>PMID:18703417</ref> <ref>PMID:18359941</ref> <ref>PMID:19854139</ref> <ref>PMID:20403326</ref> <ref>PMID:20061386</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>	+	[https://www.uniprot.org/uniprot/UB2D2_HUMAN UB2D2_HUMAN] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-48'-linked polyubiquitination. Mediates the selective degradation of short-lived and abnormal proteins. Functions in the E6/E6-AP-induced ubiquitination of p53/TP53. Mediates ubiquitination of PEX5 and autoubiquitination of STUB1 and TRAF6. Involved in the signal-induced conjugation and subsequent degradation of NFKBIA, FBXW2-mediated GCM1 ubiquitination and degradation, MDM2-dependent degradation of p53/TP53 and the activation of MAVS in the mitochondria by DDX58/RIG-I in response to viral infection. Essential for viral activation of IRF3.<ref>PMID:10329681</ref> <ref>PMID:15280377</ref> <ref>PMID:18042044</ref> <ref>PMID:18703417</ref> <ref>PMID:18359941</ref> <ref>PMID:19854139</ref> <ref>PMID:20403326</ref> <ref>PMID:20061386</ref>
		+
		+	==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 ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~RING-type E3 ubiquitin transferase~~]]	+	[[Category: Large Structures]]
-	[[Category: Day~~, C L~~]]	+	[[Category: Day CL]]
-	[[Category: Middleton~~, A J~~]]	+	[[Category: Middleton AJ]]
-	[[Category: Wright~~, J D]]~~	+	[[Category: Wright JD]]
-	~~[[Category: Backside]]~~	+
-	~~[[Category: Isopeptide-linked]]~~	+
-	~~[[Category: Open conformation]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 14:34, 6 November 2017

2017-11-06T14:34:58Z

←Older revision		Revision as of 14:34, 6 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ulh is ~~ON HOLD until Paper Publication~~	+	==Structure of RNF165 in complex with a UbcH5b~Ub conjugate==
-		+	<StructureSection load='5ulh' size='340' side='right' caption='[[5ulh]], [[Resolution\|resolution]] 1.95Å' scene=''>
-	~~Authors~~: ~~Middleton~~, A.J., ~~Day~~, C.L., ~~Wright~~, J.D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ulh]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ULH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ULH FirstGlance]. <br>
-	~~Description~~: ~~Structure~~ of ~~RNF165~~ in ~~complex with~~ a ~~UbcH5b~Ub conjugate~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ulf\|5ulf]], [[5ulk\|5ulk]]</td></tr>
-	[[Category: ~~Wright, J.D~~]]	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), UBB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RNF165 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-	[[Category: Day, C.L]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RING-type_E3_ubiquitin_transferase RING-type E3 ubiquitin transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.27 2.3.2.27] </span></td></tr>
-	[[Category: Middleton, A.J]]	+	<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=5ulh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ulh OCA], [http://pdbe.org/5ulh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ulh RCSB], [http://www.ebi.ac.uk/pdbsum/5ulh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ulh ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/UB2D2_HUMAN UB2D2_HUMAN]] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-48'-linked polyubiquitination. Mediates the selective degradation of short-lived and abnormal proteins. Functions in the E6/E6-AP-induced ubiquitination of p53/TP53. Mediates ubiquitination of PEX5 and autoubiquitination of STUB1 and TRAF6. Involved in the signal-induced conjugation and subsequent degradation of NFKBIA, FBXW2-mediated GCM1 ubiquitination and degradation, MDM2-dependent degradation of p53/TP53 and the activation of MAVS in the mitochondria by DDX58/RIG-I in response to viral infection. Essential for viral activation of IRF3.<ref>PMID:10329681</ref> <ref>PMID:15280377</ref> <ref>PMID:18042044</ref> <ref>PMID:18703417</ref> <ref>PMID:18359941</ref> <ref>PMID:19854139</ref> <ref>PMID:20403326</ref> <ref>PMID:20061386</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>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Human]]
		+	[[Category: RING-type E3 ubiquitin transferase]]
		+	[[Category: Day, C L]]
		+	[[Category: Middleton, A J]]
		+	[[Category: Wright, J D]]
		+	[[Category: Backside]]
		+	[[Category: Isopeptide-linked]]
		+	[[Category: Open conformation]]
		+	[[Category: Transferase]]

OCA at 14:34, 9 March 2017

2017-03-09T14:34:59Z

←Older revision		Revision as of 14:34, 9 March 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Middleton, A.J., Day, C.L., Wright, J.D.		Authors: Middleton, A.J., Day, C.L., Wright, J.D.

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

2017-02-01T16:47:19Z

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

←Older revision

Revision as of 16:47, 1 February 2017

OCA: New page: '''Unreleased structure''' The entry 5ulh is ON HOLD Authors: Middleton, A.J., Day, C.L., Wright, J.D. Description: Structure of RNF165 in complex with a UbcH5b~Ub conjugate [[Category...

2017-02-01T16:47:17Z

New page: '''Unreleased structure''' The entry 5ulh is ON HOLD Authors: Middleton, A.J., Day, C.L., Wright, J.D. Description: Structure of RNF165 in complex with a UbcH5b~Ub conjugate [[Category...

New page

'''Unreleased structure'''

The entry 5ulh is ON HOLD

Authors: Middleton, A.J., Day, C.L., Wright, J.D.

Description: Structure of RNF165 in complex with a UbcH5b~Ub conjugate
[[Category: Unreleased Structures]]
[[Category: Wright, J.D]]
[[Category: Day, C.L]]
[[Category: Middleton, A.J]]