6cp2 - Revision history

OCA at 15:08, 4 October 2023

2023-10-04T15:08:42Z

←Older revision		Revision as of 15:08, 4 October 2023
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	<StructureSection load='6cp2' size='340' side='right'caption='[[6cp2]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='6cp2' size='340' side='right'caption='[[6cp2]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cp2]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_33152 Atcc 33152~~] and [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CP2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6CP2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cp2]] is a 3 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=6CP2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CP2 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>UBE2L3, UBCE7, UBCH7 ([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])</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]] 2.9Å</td></tr>
-	~~<tr id='activity'><td class~~="~~sblockLbl~~">~~<b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/E2_ubiquitin~~-~~conjugating_enzyme E2 ubiquitin-conjugating enzyme]~~, ~~with EC number~~ [~~http://www.brenda-enzymes.info/php/result_flat.php4?ecno=~~2.~~3.2.23 2.3.2.23] </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=6cp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cp2 OCA], [https://pdbe.org/6cp2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cp2 RCSB], [https://www.ebi.ac.uk/pdbsum/6cp2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cp2 ProSAT]</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=6cp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cp2 OCA], [~~http~~://pdbe.org/6cp2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6cp2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6cp2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6cp2 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> [[http://www.uniprot.org/uniprot/UB2L3_HUMAN UB2L3_HUMAN]] Ubiquitin-conjugating enzyme E2 that specifically acts with HECT-type and RBR family E3 ubiquitin-protein ligases. Does not function with most RING-containing E3 ubiquitin-protein ligases because it lacks intrinsic E3-independent reactivity with lysine: in contrast, it has activity with the RBR family E3 enzymes, such as PARK2 and ARIH1, that function like function like RING-HECT hybrids. Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-11'-linked polyubiquitination. Involved in the selective degradation of short-lived and abnormal proteins. Down-regulated during the S-phase it is involved in progression through the cell cycle. Regulates nuclear hormone receptors transcriptional activity. May play a role in myelopoiesis.<ref>PMID:10888878</ref> <ref>PMID:15367689</ref> <ref>PMID:17003263</ref> <ref>PMID:19340006</ref> <ref>PMID:18946090</ref> <ref>PMID:20061386</ref> <ref>PMID:21532592</ref>	+	[https://www.uniprot.org/uniprot/Q6RCR4_LEGPN Q6RCR4_LEGPN]
	<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]]
-	*[[~~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: ~~Atcc 33152]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: E2 ubiquitin-conjugating enzyme]]~~	+
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Huang, Q~~]]	+	[[Category: Legionella pneumophila]]
-	[[Category: ~~Mao, Y~~]]	+	[[Category: Huang Q]]
-	[[Category: ~~Wasilko, D J~~]]	+	[[Category: Mao Y]]
-	[[Category: ~~Bacterial e3 ligase]]~~	+	[[Category: Wasilko DJ]]
-	~~[[Category: E2]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Ubiquitin~~]]	+

OCA at 10:48, 1 January 2020

2020-01-01T10:48:40Z

←Older revision		Revision as of 10:48, 1 January 2020
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	==SidC in complex with UbcH7~Ub==		==SidC in complex with UbcH7~Ub==
-	<StructureSection load='6cp2' size='340' side='right' caption='[[6cp2]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='6cp2' size='340' side='right'caption='[[6cp2]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6cp2]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33152 Atcc 33152] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CP2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CP2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6cp2]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33152 Atcc 33152] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CP2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CP2 FirstGlance]. <br>
Line 30:		Line 30:
	[[Category: E2 ubiquitin-conjugating enzyme]]		[[Category: E2 ubiquitin-conjugating enzyme]]
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Huang, Q]]		[[Category: Huang, Q]]
	[[Category: Mao, Y]]		[[Category: Mao, Y]]

OCA at 08:33, 21 February 2019

2019-02-21T08:33:08Z

←Older revision		Revision as of 08:33, 21 February 2019
Line 3:		Line 3:
	<StructureSection load='6cp2' size='340' side='right' caption='[[6cp2]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='6cp2' size='340' side='right' caption='[[6cp2]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cp2]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CP2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CP2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cp2]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33152 Atcc 33152] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CP2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CP2 FirstGlance]. <br>
-	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/E2_ubiquitin-conjugating_enzyme E2 ubiquitin-conjugating enzyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.23 2.3.2.23] </span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBE2L3, UBCE7, UBCH7 ([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])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/E2_ubiquitin-conjugating_enzyme E2 ubiquitin-conjugating enzyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.23 2.3.2.23] </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=6cp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cp2 OCA], [http://pdbe.org/6cp2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cp2 RCSB], [http://www.ebi.ac.uk/pdbsum/6cp2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cp2 ProSAT]</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=6cp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cp2 OCA], [http://pdbe.org/6cp2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cp2 RCSB], [http://www.ebi.ac.uk/pdbsum/6cp2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cp2 ProSAT]</span></td></tr>
	</table>		</table>
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6cp2" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6cp2" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ubiquitin\|Ubiquitin]]
		+	*[[Ubiquitin conjugating enzyme\|Ubiquitin conjugating enzyme]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 33152]]
	[[Category: E2 ubiquitin-conjugating enzyme]]		[[Category: E2 ubiquitin-conjugating enzyme]]
		+	[[Category: Human]]
	[[Category: Huang, Q]]		[[Category: Huang, Q]]
	[[Category: Mao, Y]]		[[Category: Mao, Y]]

OCA at 18:47, 1 August 2018

2018-08-01T18:47:53Z

←Older revision		Revision as of 18:47, 1 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6cp2 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==SidC in complex with UbcH7~Ub==
		+	<StructureSection load='6cp2' size='340' side='right' caption='[[6cp2]], [[Resolution\|resolution]] 2.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6cp2]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CP2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CP2 FirstGlance]. <br>
		+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/E2_ubiquitin-conjugating_enzyme E2 ubiquitin-conjugating enzyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.23 2.3.2.23] </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=6cp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cp2 OCA], [http://pdbe.org/6cp2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cp2 RCSB], [http://www.ebi.ac.uk/pdbsum/6cp2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cp2 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> [[http://www.uniprot.org/uniprot/UB2L3_HUMAN UB2L3_HUMAN]] Ubiquitin-conjugating enzyme E2 that specifically acts with HECT-type and RBR family E3 ubiquitin-protein ligases. Does not function with most RING-containing E3 ubiquitin-protein ligases because it lacks intrinsic E3-independent reactivity with lysine: in contrast, it has activity with the RBR family E3 enzymes, such as PARK2 and ARIH1, that function like function like RING-HECT hybrids. Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-11'-linked polyubiquitination. Involved in the selective degradation of short-lived and abnormal proteins. Down-regulated during the S-phase it is involved in progression through the cell cycle. Regulates nuclear hormone receptors transcriptional activity. May play a role in myelopoiesis.<ref>PMID:10888878</ref> <ref>PMID:15367689</ref> <ref>PMID:17003263</ref> <ref>PMID:19340006</ref> <ref>PMID:18946090</ref> <ref>PMID:20061386</ref> <ref>PMID:21532592</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The causative agent of Legionnaires' disease, Legionella pneumophila, delivers more than 330 virulent effectors to its host to establish an intracellular membrane-bound organelle called the Legionella containing vacuole. Among the army of Legionella effectors, SidC and its paralog SdcA have been identified as novel bacterial ubiquitin (Ub) E3 ligases. To gain insight into the molecular mechanism of SidC/SdcA as Ub ligases, we determined the crystal structures of a binary complex of the N-terminal catalytic SNL domain of SdcA with its cognate E2 UbcH5C and a ternary complex consisting of the SNL domain of SidC with the Ub-linked E2 UbcH7. These two structures reveal the molecular determinants governing the Ub transfer cascade catalyzed by SidC. Together, our data support a common mechanism in the Ub transfer cascade in which the donor Ub is immobilized with its C-terminal tail locked in an extended conformation, priming the donor Ub for catalysis.

-	~~Authors: Wasilko, D.J~~., ~~Huang~~, Q., Mao, Y.	+	Insights into the ubiquitin transfer cascade catalyzed by the Legionella effector SidC.,Wasilko DJ, Huang Q, Mao Y Elife. 2018 Jul 17;7. pii: 36154. doi: 10.7554/eLife.36154. PMID:30015617<ref>PMID:30015617</ref>

-	~~Description~~: ~~SidC in complex with UbcH7~Ub~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6cp2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: E2 ubiquitin-conjugating enzyme]]
	[[Category: Huang, Q]]		[[Category: Huang, Q]]
	[[Category: Mao, Y]]		[[Category: Mao, Y]]
-	[[Category: Wasilko, D.J]]	+	[[Category: Wasilko, D J]]
		+	[[Category: Bacterial e3 ligase]]
		+	[[Category: E2]]
		+	[[Category: Ligase]]
		+	[[Category: Ubiquitin]]

OCA at 03:58, 30 May 2018

2018-05-30T03:58:35Z

←Older revision		Revision as of 03:58, 30 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6cp2 is ON HOLD	+	The entry 6cp2 is ON HOLD until Paper Publication

	Authors: Wasilko, D.J., Huang, Q., Mao, Y.		Authors: Wasilko, D.J., Huang, Q., Mao, Y.

OCA: Protected "6cp2" [edit=sysop:move=sysop]

2018-03-21T06:11:44Z

Protected "6cp2" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:11, 21 March 2018

OCA: New page: '''Unreleased structure''' The entry 6cp2 is ON HOLD Authors: Wasilko, D.J., Huang, Q., Mao, Y. Description: SidC in complex with UbcH7~Ub Category: Unreleased Structures [[Categor...

2018-03-21T06:11:43Z

New page: '''Unreleased structure''' The entry 6cp2 is ON HOLD Authors: Wasilko, D.J., Huang, Q., Mao, Y. Description: SidC in complex with UbcH7~Ub Category: Unreleased Structures [[Categor...

New page

'''Unreleased structure'''

The entry 6cp2 is ON HOLD

Authors: Wasilko, D.J., Huang, Q., Mao, Y.

Description: SidC in complex with UbcH7~Ub
[[Category: Unreleased Structures]]
[[Category: Huang, Q]]
[[Category: Mao, Y]]
[[Category: Wasilko, D.J]]