7bol - Revision history

OCA at 15:22, 29 November 2023

OCA — Wed, 29 Nov 2023 15:22:35 GMT

←Older revision		Revision as of 15:22, 29 November 2023
Line 3:		Line 3:
	<StructureSection load='7bol' size='340' side='right'caption='[[7bol]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='7bol' size='340' side='right'caption='[[7bol]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7bol]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BOL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7bol]] 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=7BOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BOL FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~UBE2D2~~, ~~PUBC1, UBC4, UBC5B, UBCH4, UBCH5B (~~[~~https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=9606 HUMAN])~~</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]] 1.797Å</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=7bol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bol OCA], [https://pdbe.org/7bol PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bol RCSB], [https://www.ebi.ac.uk/pdbsum/7bol PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bol 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=7bol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bol OCA], [https://pdbe.org/7bol PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bol RCSB], [https://www.ebi.ac.uk/pdbsum/7bol PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bol ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[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>	+	[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>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 7bol" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7bol" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[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: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chi, S W]]	+	[[Category: Chi S-W]]
-	[[Category: Lee~~, S O~~]]	+	[[Category: Lee SO]]
-	[[Category: Ryu~~, K S]]~~	+	[[Category: Ryu KS]]
-	~~[[Category: Structural protein]]~~	+
-	~~[[Category: Ube2d2]]~~	+
-	~~[[Category: Ubiquitin-conjugating enzyme~~]]	+

OCA at 03:03, 21 April 2022

OCA — Thu, 21 Apr 2022 03:03:28 GMT

←Older revision		Revision as of 03:03, 21 April 2022
Line 1:		Line 1:

	==ubiquitin-conjugating enzyme, Ube2D2==		==ubiquitin-conjugating enzyme, Ube2D2==
-	<StructureSection load='7bol' size='340' side='right'caption='[[7bol]]' scene=''>	+	<StructureSection load='7bol' size='340' side='right'caption='[[7bol]], [[Resolution\|resolution]] 1.80Å' 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=7BOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BOL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7bol]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BOL 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=7bol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bol OCA], [https://pdbe.org/7bol PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bol RCSB], [https://www.ebi.ac.uk/pdbsum/7bol PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bol ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B ([https://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=7bol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bol OCA], [https://pdbe.org/7bol PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bol RCSB], [https://www.ebi.ac.uk/pdbsum/7bol PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bol ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The RING domain of MUL1 (RINGMUL1 ) alone mediates ubiquitylation of the p53-transactivation domain (TADp53 ). To elucidate the mechanism underlying the simultaneous recruitment of UBE2D2 and the substrate TADp53 by RINGMUL1 , we determined the complex structure of RINGMUL1 :UBE2D2 and studied the interaction between RINGMUL1 and TADp53 in the presence of UBE2D2-UB thioester (UBE2D2~UB) mimetics. The RINGMUL1 -binding induced the closed conformation of UBE2D2(S22R/C85S) -UB(K48R) oxyester (UBE2D2(RS) -UB(R) OE ), and strongly accelerated its hydrolysis, which was suppressed by the additional N77A-mutation of UBE2D2. Interestingly, UBE2D2(S22R/N77A/C85S) -UB(K48R) oxyester (UBE2D2(RAS) -UB(R) OE ) already formed a closed conformation in the absence of RINGMUL1 . Although TADp53 exhibited weak binding for RINGMUL1 or UBE2D2 alone, its binding affinity was enhanced and even further for RINGMUL1 :UBE2D2 and RINGMUL1 :UBE2D2(RAS) -UB(R) OE , respectively. The recognition of TADp53 by RINGMUL1 as a complex with UBE2D2~UB is related to the multivalency of the binding events and underlies the ability of RINGMUL1 to ubiquitylate the intrinsically disordered protein, TADp53 .
		+
		+	MUL1-RING recruits the substrate, p53-TAD as a complex with UBE2D2-UB conjugate.,Lee MS, Lee SO, Choi J, Ryu M, Lee MK, Kim JH, Hwang E, Lee CK, Chi SW, Ryu KS FEBS J. 2022 Jan 19. doi: 10.1111/febs.16360. PMID:35048531<ref>PMID:35048531</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7bol" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chi S-W]]	+	[[Category: Chi, S W]]
-	[[Category: Lee SO]]	+	[[Category: Lee, S O]]
-	[[Category: Ryu KS]]	+	[[Category: Ryu, K S]]
		+	[[Category: Structural protein]]
		+	[[Category: Ube2d2]]
		+	[[Category: Ubiquitin-conjugating enzyme]]

OCA at 06:39, 24 March 2021

OCA — Wed, 24 Mar 2021 06:39:38 GMT

←Older revision		Revision as of 06:39, 24 March 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7bol ~~is ON HOLD until Paper Publication~~	+	==ubiquitin-conjugating enzyme, Ube2D2==
-		+	<StructureSection load='7bol' size='340' side='right'caption='[[7bol]]' scene=''>
-	~~Authors~~: ~~Lee~~, S.O., ~~Ryu~~, K.S., ~~Chi~~, S.-W.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BOL FirstGlance]. <br>
-	~~Description: ubiquitin-conjugating enzyme, Ube2D2~~	+	</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=7bol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bol OCA], [https://pdbe.org/7bol PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bol RCSB], [https://www.ebi.ac.uk/pdbsum/7bol PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bol ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Chi, S.-W]]	+	__TOC__
-	[[Category: Lee~~, S.O~~]]	+	</StructureSection>
-	[[Category: Ryu~~, K.S~~]]	+	[[Category: Large Structures]]
		+	[[Category: Chi S-W]]
		+	[[Category: Lee SO]]
		+	[[Category: Ryu KS]]

OCA at 05:26, 4 November 2020

OCA — Wed, 04 Nov 2020 05:26:02 GMT

←Older revision		Revision as of 05:26, 4 November 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Lee, S.O., Ryu, K.S., Chi, S.-W.		Authors: Lee, S.O., Ryu, K.S., Chi, S.-W.
Line 7:		Line 7:
	Description: ubiquitin-conjugating enzyme, Ube2D2		Description: ubiquitin-conjugating enzyme, Ube2D2
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Lee, S.O]]
	[[Category: Chi, S.-W]]		[[Category: Chi, S.-W]]
		+	[[Category: Lee, S.O]]
	[[Category: Ryu, K.S]]		[[Category: Ryu, K.S]]

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

OCA — Fri, 27 Mar 2020 08:40:57 GMT

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

←Older revision

Revision as of 08:40, 27 March 2020

OCA: New page: '''Unreleased structure''' The entry 7bol is ON HOLD Authors: Lee, S.O., Ryu, K.S., Chi, S.-W. Description: ubiquitin-conjugating enzyme, Ube2D2 Category: Unreleased Structures [[C...

OCA — Fri, 27 Mar 2020 08:40:55 GMT

New page: '''Unreleased structure''' The entry 7bol is ON HOLD Authors: Lee, S.O., Ryu, K.S., Chi, S.-W. Description: ubiquitin-conjugating enzyme, Ube2D2 Category: Unreleased Structures [[C...

New page

'''Unreleased structure'''

The entry 7bol is ON HOLD

Authors: Lee, S.O., Ryu, K.S., Chi, S.-W.

Description: ubiquitin-conjugating enzyme, Ube2D2
[[Category: Unreleased Structures]]
[[Category: Lee, S.O]]
[[Category: Chi, S.-W]]
[[Category: Ryu, K.S]]