3l1z - Revision history

OCA at 08:28, 6 September 2023

OCA — Wed, 06 Sep 2023 08:28:37 GMT

←Older revision		Revision as of 08:28, 6 September 2023
Line 1:		Line 1:

	==Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme==		==Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme==
-	<StructureSection load='3l1z' size='340' side='right' caption='[[3l1z]], [[Resolution\|resolution]] 3.17Å' scene=''>	+	<StructureSection load='3l1z' size='340' side='right'caption='[[3l1z]], [[Resolution\|resolution]] 3.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3l1z]] is a 2 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=3L1Z OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3L1Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3l1z]] is a 2 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=3L1Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3L1Z FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[3l1x\|3l1x]], [[3l1y\|3l1y]]</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]] 3.17Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">UBE2D3, UBCH5C ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=9606 HUMAN]), UBE4B, HDNB1, KIAA0684, UFD2 ([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=3l1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l1z OCA], [https://pdbe.org/3l1z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3l1z RCSB], [https://www.ebi.ac.uk/pdbsum/3l1z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3l1z 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/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] </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=3l1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l1z OCA], [~~http~~://pdbe.org/3l1z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3l1z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3l1z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3l1z ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/UB2D3_HUMAN UB2D3_HUMAN]] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-11'-, as well as 'Lys-48'-linked polyubiquitination. Cooperates with the E2 CDC34 and the SCF(FBXW11) E3 ligase complex for the polyubiquitination of NFKBIA leading to its subsequent proteasomal degradation. Acts as an initiator E2, priming the phosphorylated NFKBIA target at positions 'Lys-21' and/or 'Lys-22' with a monoubiquitin. Ubiquitin chain elongation is then performed by CDC34, building ubiquitin chains from the UBE2D3-primed NFKBIA-linked ubiquitin. Acts also as an initiator E2, in conjunction with RNF8, for the priming of PCNA. Monoubiquitination of PCNA, and its subsequent polyubiquitination, are essential events in the operation of the DNA damage tolerance (DDT) pathway that is activated after DNA damage caused by UV or chemical agents during S-phase. Associates with the BRCA1/BARD1 E3 ligase complex to perform ubiquitination at DNA damage sites following ionizing radiation leading to DNA repair. Targets DAPK3 for ubiquitination which influences promyelocytic leukemia protein nuclear body (PML-NB) formation in the nucleus. In conjunction with the MDM2 and TOPORS E3 ligases, functions ubiquitination of p53/TP53. Supports NRDP1-mediated ubiquitination and degradation of ERBB3 and of BRUCE which triggers apoptosis. In conjunction with the CBL E3 ligase, targets EGFR for polyubiquitination at the plasma membrane as well as during its internalization and transport on endosomes. In conjunction with the STUB1 E3 quality control E3 ligase, ubiquitinates unfolded proteins to catalyze their immediate destruction (By similarity).<ref>PMID:10329681</ref> <ref>PMID:11743028</ref> <ref>PMID:12646252</ref> <ref>PMID:15247280</ref> <ref>PMID:15280377</ref> <ref>PMID:15496420</ref> <ref>PMID:16628214</ref> <ref>PMID:18515077</ref> <ref>PMID:18948756</ref> <ref>PMID:18508924</ref> <ref>PMID:18284575</ref> <ref>PMID:20061386</ref> <ref>PMID:20347421</ref> <ref>PMID:21532592</ref> [[http://www.uniprot.org/uniprot/UBE4B_HUMAN UBE4B_HUMAN]] Binds to the ubiquitin moieties of preformed conjugates and catalyzes ubiquitin chain assembly in conjunction with E1, E2, and E3 (By similarity).	+	[https://www.uniprot.org/uniprot/UB2D3_HUMAN UB2D3_HUMAN] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-11'-, as well as 'Lys-48'-linked polyubiquitination. Cooperates with the E2 CDC34 and the SCF(FBXW11) E3 ligase complex for the polyubiquitination of NFKBIA leading to its subsequent proteasomal degradation. Acts as an initiator E2, priming the phosphorylated NFKBIA target at positions 'Lys-21' and/or 'Lys-22' with a monoubiquitin. Ubiquitin chain elongation is then performed by CDC34, building ubiquitin chains from the UBE2D3-primed NFKBIA-linked ubiquitin. Acts also as an initiator E2, in conjunction with RNF8, for the priming of PCNA. Monoubiquitination of PCNA, and its subsequent polyubiquitination, are essential events in the operation of the DNA damage tolerance (DDT) pathway that is activated after DNA damage caused by UV or chemical agents during S-phase. Associates with the BRCA1/BARD1 E3 ligase complex to perform ubiquitination at DNA damage sites following ionizing radiation leading to DNA repair. Targets DAPK3 for ubiquitination which influences promyelocytic leukemia protein nuclear body (PML-NB) formation in the nucleus. In conjunction with the MDM2 and TOPORS E3 ligases, functions ubiquitination of p53/TP53. Supports NRDP1-mediated ubiquitination and degradation of ERBB3 and of BRUCE which triggers apoptosis. In conjunction with the CBL E3 ligase, targets EGFR for polyubiquitination at the plasma membrane as well as during its internalization and transport on endosomes. In conjunction with the STUB1 E3 quality control E3 ligase, ubiquitinates unfolded proteins to catalyze their immediate destruction (By similarity).<ref>PMID:10329681</ref> <ref>PMID:11743028</ref> <ref>PMID:12646252</ref> <ref>PMID:15247280</ref> <ref>PMID:15280377</ref> <ref>PMID:15496420</ref> <ref>PMID:16628214</ref> <ref>PMID:18515077</ref> <ref>PMID:18948756</ref> <ref>PMID:18508924</ref> <ref>PMID:18284575</ref> <ref>PMID:20061386</ref> <ref>PMID:20347421</ref> <ref>PMID:21532592</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
-	*[[~~Ubiquitin~~ conjugating enzyme\|~~Ubiquitin~~ conjugating enzyme]]	+	*[[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: ~~Ubiquitin--protein ligase~~]]	+	[[Category: Large Structures]]
-	[[Category: Benirschke, R]]	+	[[Category: Benirschke R]]
-	[[Category: Mer, G]]	+	[[Category: Mer G]]
-	[[Category: Thompson~~, J R]]~~	+	[[Category: Thompson JR]]
-	~~[[Category: E2 ubiquitin conjugating enzyme]]~~	+
-	~~[[Category: E4b]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: U-box ubiquitin ligase]]~~	+
-	~~[[Category: Ubch5c]]~~	+
-	~~[[Category: Ubl conjugation pathway]]~~	+
-	~~[[Category: Ufd2a~~]]	+

OCA at 07:18, 2 January 2019

OCA — Wed, 02 Jan 2019 07:18:15 GMT

←Older revision		Revision as of 07:18, 2 January 2019
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l1/3l1z_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l1/3l1z_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 10:46, 4 August 2016

OCA — Thu, 04 Aug 2016 10:46:03 GMT

←Older revision		Revision as of 10:46, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme==		==Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme==
	<StructureSection load='3l1z' size='340' side='right' caption='[[3l1z]], [[Resolution\|resolution]] 3.17Å' scene=''>		<StructureSection load='3l1z' size='340' side='right' caption='[[3l1z]], [[Resolution\|resolution]] 3.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3l1z]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L1Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3L1Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3l1z]] is a 2 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=3L1Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3L1Z FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3l1x\|3l1x]], [[3l1y\|3l1y]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3l1x\|3l1x]], [[3l1y\|3l1y]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBE2D3, UBCH5C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~]), UBE4B, HDNB1, KIAA0684, UFD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBE2D3, UBCH5C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), UBE4B, HDNB1, KIAA0684, UFD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] </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=3l1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l1z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3l1z RCSB], [http://www.ebi.ac.uk/pdbsum/3l1z PDBsum]</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=3l1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l1z OCA], [http://pdbe.org/3l1z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3l1z RCSB], [http://www.ebi.ac.uk/pdbsum/3l1z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3l1z ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3l1z ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3l1z" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Ubiquitin--protein ligase]]		[[Category: Ubiquitin--protein ligase]]
	[[Category: Benirschke, R]]		[[Category: Benirschke, R]]

OCA at 08:29, 25 December 2014

OCA — Thu, 25 Dec 2014 08:29:46 GMT

←Older revision		Revision as of 08:29, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3l1z]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L1Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3L1Z FirstGlance]. <br>		<table><tr><td colspan='2'>[[3l1z]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L1Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3L1Z FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3l1x\|3l1x]], [[3l1y\|3l1y]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3l1x\|3l1x]], [[3l1y\|3l1y]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBE2D3, UBCH5C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), UBE4B, HDNB1, KIAA0684, UFD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBE2D3, UBCH5C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), UBE4B, HDNB1, KIAA0684, UFD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3l1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l1z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3l1z RCSB], [http://www.ebi.ac.uk/pdbsum/3l1z PDBsum]</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=3l1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l1z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3l1z RCSB], [http://www.ebi.ac.uk/pdbsum/3l1z PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/UB2D3_HUMAN UB2D3_HUMAN]] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-11'-, as well as 'Lys-48'-linked polyubiquitination. Cooperates with the E2 CDC34 and the SCF(FBXW11) E3 ligase complex for the polyubiquitination of NFKBIA leading to its subsequent proteasomal degradation. Acts as an initiator E2, priming the phosphorylated NFKBIA target at positions 'Lys-21' and/or 'Lys-22' with a monoubiquitin. Ubiquitin chain elongation is then performed by CDC34, building ubiquitin chains from the UBE2D3-primed NFKBIA-linked ubiquitin. Acts also as an initiator E2, in conjunction with RNF8, for the priming of PCNA. Monoubiquitination of PCNA, and its subsequent polyubiquitination, are essential events in the operation of the DNA damage tolerance (DDT) pathway that is activated after DNA damage caused by UV or chemical agents during S-phase. Associates with the BRCA1/BARD1 E3 ligase complex to perform ubiquitination at DNA damage sites following ionizing radiation leading to DNA repair. Targets DAPK3 for ubiquitination which influences promyelocytic leukemia protein nuclear body (PML-NB) formation in the nucleus. In conjunction with the MDM2 and TOPORS E3 ligases, functions ubiquitination of p53/TP53. Supports NRDP1-mediated ubiquitination and degradation of ERBB3 and of BRUCE which triggers apoptosis. In conjunction with the CBL E3 ligase, targets EGFR for polyubiquitination at the plasma membrane as well as during its internalization and transport on endosomes. In conjunction with the STUB1 E3 quality control E3 ligase, ubiquitinates unfolded proteins to catalyze their immediate destruction (By similarity).<ref>PMID:10329681</ref> <ref>PMID:11743028</ref> <ref>PMID:12646252</ref> <ref>PMID:15247280</ref> <ref>PMID:15280377</ref> <ref>PMID:15496420</ref> <ref>PMID:16628214</ref> <ref>PMID:18515077</ref> <ref>PMID:18948756</ref> <ref>PMID:18508924</ref> <ref>PMID:18284575</ref> <ref>PMID:20061386</ref> <ref>PMID:20347421</ref> <ref>PMID:21532592</ref> [[http://www.uniprot.org/uniprot/UBE4B_HUMAN UBE4B_HUMAN]] Binds to the ubiquitin moieties of preformed conjugates and catalyzes ubiquitin chain assembly in conjunction with E1, E2, and E3 (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 24:		Line 26:
	Molecular basis for the association of human E4B U box ubiquitin ligase with E2-conjugating enzymes UbcH5c and Ubc4.,Benirschke RC, Thompson JR, Nomine Y, Wasielewski E, Juranic N, Macura S, Hatakeyama S, Nakayama KI, Botuyan MV, Mer G Structure. 2010 Aug 11;18(8):955-65. PMID:20696396<ref>PMID:20696396</ref>		Molecular basis for the association of human E4B U box ubiquitin ligase with E2-conjugating enzymes UbcH5c and Ubc4.,Benirschke RC, Thompson JR, Nomine Y, Wasielewski E, Juranic N, Macura S, Hatakeyama S, Nakayama KI, Botuyan MV, Mer G Structure. 2010 Aug 11;18(8):955-65. PMID:20696396<ref>PMID:20696396</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+
		+	==See Also==
		+	*[[Ubiquitin conjugating enzyme\|Ubiquitin conjugating enzyme]]
	== References ==		== References ==
	<references/>		<references/>
Line 32:		Line 37:
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Ubiquitin--protein ligase]]		[[Category: Ubiquitin--protein ligase]]
-	[[Category: Benirschke, R.]]	+	[[Category: Benirschke, R]]
-	[[Category: Mer, G.]]	+	[[Category: Mer, G]]
-	[[Category: Thompson, J R.]]	+	[[Category: Thompson, J R]]
	[[Category: E2 ubiquitin conjugating enzyme]]		[[Category: E2 ubiquitin conjugating enzyme]]
	[[Category: E4b]]		[[Category: E4b]]

OCA at 09:50, 21 May 2014

OCA — Wed, 21 May 2014 09:50:29 GMT

←Older revision		Revision as of 09:50, 21 May 2014
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-	[[~~Image:~~3l1z.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme==
		+	<StructureSection load='3l1z' size='340' side='right' caption='[[3l1z]], [[Resolution\|resolution]] 3.17Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3l1z]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L1Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3L1Z FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3l1x\|3l1x]], [[3l1y\|3l1y]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBE2D3, UBCH5C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), UBE4B, HDNB1, KIAA0684, UFD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3l1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l1z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3l1z RCSB], [http://www.ebi.ac.uk/pdbsum/3l1z PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l1/3l1z_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Human E4B, also called UFD2a, is a U box-containing protein that functions as an E3 ubiquitin ligase and an E4 polyubiquitin chain elongation factor. E4B is thought to participate in the proteasomal degradation of misfolded or damaged proteins through association with chaperones. The U box domain is an anchor site for E2 ubiquitin-conjugating enzymes, but little is known of the binding mechanism. Using X-ray crystallography and NMR spectroscopy, we determined the structures of E4B U box free and bound to UbcH5c and Ubc4 E2s. Whereas previously characterized U box domains are homodimeric, we show that E4B U box is a monomer stabilized by a network of hydrogen bonds identified from scalar coupling measurements. These structural studies, complemented by calorimetry- and NMR-based binding assays, suggest an allosteric regulation of UbcH5c and Ubc4 by E4B U box and provide a molecular basis to understand how the ubiquitylation machinery involving E4B assembles.

-	<!--	+	Molecular basis for the association of human E4B U box ubiquitin ligase with E2-conjugating enzymes UbcH5c and Ubc4.,Benirschke RC, Thompson JR, Nomine Y, Wasielewski E, Juranic N, Macura S, Hatakeyama S, Nakayama KI, Botuyan MV, Mer G Structure. 2010 Aug 11;18(8):955-65. PMID:20696396<ref>PMID:20696396</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3l1z"~~, ~~creates the "~~Structure ~~Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~	+
-	~~or leave the SCENE parameter empty for the default display~~.	+
-	-->	+
-	~~{{STRUCTURE_3l1z\| PDB=3l1z \| SCENE= }}~~	+

-	~~===Crystal structure~~ of the U~~-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_20696396}}, adds the Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 20696396 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_20696396}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3l1z]] is a 2 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L1Z OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:020696396<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Ubiquitin--protein ligase]]		[[Category: Ubiquitin--protein ligase]]

OCA: Protected "3l1z" [edit=sysop:move=sysop]

OCA — Wed, 28 Dec 2011 06:15:31 GMT

Protected "3l1z" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:15, 28 December 2011

OCA at 06:15, 28 December 2011

OCA — Wed, 28 Dec 2011 06:15:29 GMT

←Older revision		Revision as of 06:15, 28 December 2011
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-	{{Seed}}
	[[Image:3l1z.png\|left\|200px]]		[[Image:3l1z.png\|left\|200px]]

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	==About this Structure==		==About this Structure==
-	~~3L1Z~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L1Z OCA].	+	[[3l1z]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L1Z OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20696396~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020696396</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Ubiquitin--protein ligase]]		[[Category: Ubiquitin--protein ligase]]
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	[[Category: Ubl conjugation pathway]]		[[Category: Ubl conjugation pathway]]
	[[Category: Ufd2a]]		[[Category: Ufd2a]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 25 08:24:09 2010''

OCA at 04:16, 25 August 2010

OCA — Wed, 25 Aug 2010 04:16:18 GMT

←Older revision		Revision as of 04:16, 25 August 2010
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	===Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme===		===Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20696396}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20696396 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20696396}}

	==About this Structure==		==About this Structure==
	3L1Z is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L1Z OCA].		3L1Z is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L1Z OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20696396</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Ubiquitin--protein ligase]]		[[Category: Ubiquitin--protein ligase]]
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	[[Category: Ufd2a]]		[[Category: Ufd2a]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jul 7 07~~:51:41 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 25 08:24:09 2010''

OCA at 03:46, 7 July 2010

OCA — Wed, 07 Jul 2010 03:46:09 GMT

←Older revision		Revision as of 03:46, 7 July 2010
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	{{Seed}}		{{Seed}}
-	[[Image:3l1z.~~jpg~~\|left\|200px]]	+	[[Image:3l1z.png\|left\|200px]]

	<!--		<!--
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	[[Category: Ufd2a]]		[[Category: Ufd2a]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~May~~ ~~5 12~~:08:03 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 7 07:51:41 2010''

OCA at 09:08, 5 May 2010

OCA — Wed, 05 May 2010 09:08:05 GMT

←Older revision		Revision as of 09:08, 5 May 2010
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3l1z.jpg\|left\|200px]]

-	The ~~entry 3l1z~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3l1z", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3l1z\| PDB=3l1z \| SCENE= }}

-	~~Authors: Benirschke, R., Thompson, J.R., Mer, G.~~	+	===Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme===

-	Description: Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Apr~~ ~~7 10~~:19:05 2010''	+	==About this Structure==
		+	3L1Z is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L1Z OCA].
		+	[[Category: Homo sapiens]]
		+	[[Category: Ubiquitin--protein ligase]]
		+	[[Category: Benirschke, R.]]
		+	[[Category: Mer, G.]]
		+	[[Category: Thompson, J R.]]
		+	[[Category: E2 ubiquitin conjugating enzyme]]
		+	[[Category: E4b]]
		+	[[Category: Ligase]]
		+	[[Category: U-box ubiquitin ligase]]
		+	[[Category: Ubch5c]]
		+	[[Category: Ubl conjugation pathway]]
		+	[[Category: Ufd2a]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 5 12:08:03 2010''