5yim - Revision history

OCA at 10:23, 27 March 2024

OCA — Wed, 27 Mar 2024 10:23:38 GMT

←Older revision		Revision as of 10:23, 27 March 2024
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	<StructureSection load='5yim' size='340' side='right'caption='[[5yim]], [[Resolution\|resolution]] 3.39Å' scene=''>		<StructureSection load='5yim' size='340' side='right'caption='[[5yim]], [[Resolution\|resolution]] 3.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yim]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_33152 Atcc 33152~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YIM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yim]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Legionella_pneumophila Legionella pneumophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YIM FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5yij\|5yij]]~~, [[~~5yik~~\|~~5yik~~]]</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]] 3.394Å</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=5yim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yim OCA], [~~http~~://pdbe.org/5yim PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yim RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yim PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yim 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=5yim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yim OCA], [https://pdbe.org/5yim PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yim RCSB], [https://www.ebi.ac.uk/pdbsum/5yim PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yim ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q6RCR0_LEGPN Q6RCR0_LEGPN]
-	Protein ubiquitination is a multifaceted post-translational modification that controls almost every process in eukaryotic cells. Recently, the Legionella effector SdeA was reported to mediate a unique phosphoribosyl-linked ubiquitination through successive modifications of the Arg42 of ubiquitin (Ub) by its mono-ADP-ribosyltransferase (mART) and phosphodiesterase (PDE) domains. However, the mechanisms of SdeA-mediated Ub modification and phosphoribosyl-linked ubiquitination remain unknown. Here we report the structures of SdeA in its ligand-free, Ub-bound and Ub-NADH-bound states. The structures reveal that the mART and PDE domains of SdeA form a catalytic domain over its C-terminal region. Upon Ub binding, the canonical ADP-ribosyltransferase toxin turn-turn (ARTT) and phosphate-nicotinamide (PN) loops in the mART domain of SdeA undergo marked conformational changes. The Ub Arg72 might act as a 'probe' that interacts with the mART domain first, and then movements may occur in the side chains of Arg72 and Arg42 during the ADP-ribosylation of Ub. Our study reveals the mechanism of SdeA-mediated Ub modification and provides a framework for further investigations into the phosphoribosyl-linked ubiquitination process.	+
-		+
-	Structural basis of ubiquitin modification by the Legionella effector SdeA.,Dong Y, Mu Y, Xie Y, Zhang Y, Han Y, Zhou Y, Wang W, Liu Z, Wu M, Wang H, Pan M, Xu N, Xu CQ, Yang M, Fan S, Deng H, Tan T, Liu X, Liu L, Li J, Wang J, Fang X, Feng Y Nature. 2018 May;557(7707):~~674-678. doi: 10.1038~~/~~s41586-018-0146-7. Epub 2018 May, 23. PMID:29795342<ref>PMID:29795342<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5yim" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 33152]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Dong, Y~~]]	+	[[Category: Legionella pneumophila]]
-	[[Category: ~~Feng,~~ Y]]	+	[[Category: Dong Y]]
-	[[Category: ~~Wang, W~~]]	+	[[Category: Feng Y]]
-	[[Category: ~~Monomer]]~~	+	[[Category: Wang W]]
-	~~[[Category: Multi-domain protein]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:20, 21 October 2020

OCA — Wed, 21 Oct 2020 09:20:21 GMT

←Older revision		Revision as of 09:20, 21 October 2020
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	==Structure of a Legionella effector==		==Structure of a Legionella effector==
-	<StructureSection load='5yim' size='340' side='right' caption='[[5yim]], [[Resolution\|resolution]] 3.39Å' scene=''>	+	<StructureSection load='5yim' size='340' side='right'caption='[[5yim]], [[Resolution\|resolution]] 3.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yim]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33152 Atcc 33152]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YIM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yim]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33152 Atcc 33152]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YIM FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5yij\|5yij]], [[5yik\|5yik]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5yij\|5yij]], [[5yik\|5yik]]</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=5yim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yim OCA], [http://pdbe.org/5yim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yim RCSB], [http://www.ebi.ac.uk/pdbsum/5yim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yim 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=5yim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yim OCA], [http://pdbe.org/5yim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yim RCSB], [http://www.ebi.ac.uk/pdbsum/5yim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yim ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Atcc 33152]]		[[Category: Atcc 33152]]
		+	[[Category: Large Structures]]
	[[Category: Dong, Y]]		[[Category: Dong, Y]]
	[[Category: Feng, Y]]		[[Category: Feng, Y]]

OCA at 08:06, 14 June 2018

OCA — Thu, 14 Jun 2018 08:06:14 GMT

←Older revision		Revision as of 08:06, 14 June 2018
Line 3:		Line 3:
	<StructureSection load='5yim' size='340' side='right' caption='[[5yim]], [[Resolution\|resolution]] 3.39Å' scene=''>		<StructureSection load='5yim' size='340' side='right' caption='[[5yim]], [[Resolution\|resolution]] 3.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yim]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YIM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yim]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33152 Atcc 33152]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YIM FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5yij\|5yij]], [[5yik\|5yik]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5yij\|5yij]], [[5yik\|5yik]]</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=5yim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yim OCA], [http://pdbe.org/5yim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yim RCSB], [http://www.ebi.ac.uk/pdbsum/5yim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yim 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=5yim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yim OCA], [http://pdbe.org/5yim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yim RCSB], [http://www.ebi.ac.uk/pdbsum/5yim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yim ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Protein ubiquitination is a multifaceted post-translational modification that controls almost every process in eukaryotic cells. Recently, the Legionella effector SdeA was reported to mediate a unique phosphoribosyl-linked ubiquitination through successive modifications of the Arg42 of ubiquitin (Ub) by its mono-ADP-ribosyltransferase (mART) and phosphodiesterase (PDE) domains. However, the mechanisms of SdeA-mediated Ub modification and phosphoribosyl-linked ubiquitination remain unknown. Here we report the structures of SdeA in its ligand-free, Ub-bound and Ub-NADH-bound states. The structures reveal that the mART and PDE domains of SdeA form a catalytic domain over its C-terminal region. Upon Ub binding, the canonical ADP-ribosyltransferase toxin turn-turn (ARTT) and phosphate-nicotinamide (PN) loops in the mART domain of SdeA undergo marked conformational changes. The Ub Arg72 might act as a 'probe' that interacts with the mART domain first, and then movements may occur in the side chains of Arg72 and Arg42 during the ADP-ribosylation of Ub. Our study reveals the mechanism of SdeA-mediated Ub modification and provides a framework for further investigations into the phosphoribosyl-linked ubiquitination process.
		+
		+	Structural basis of ubiquitin modification by the Legionella effector SdeA.,Dong Y, Mu Y, Xie Y, Zhang Y, Han Y, Zhou Y, Wang W, Liu Z, Wu M, Wang H, Pan M, Xu N, Xu CQ, Yang M, Fan S, Deng H, Tan T, Liu X, Liu L, Li J, Wang J, Fang X, Feng Y Nature. 2018 May;557(7707):674-678. doi: 10.1038/s41586-018-0146-7. Epub 2018 May, 23. PMID:29795342<ref>PMID:29795342</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5yim" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 33152]]
	[[Category: Dong, Y]]		[[Category: Dong, Y]]
	[[Category: Feng, Y]]		[[Category: Feng, Y]]

OCA at 05:29, 30 May 2018

OCA — Wed, 30 May 2018 05:29:09 GMT

←Older revision		Revision as of 05:29, 30 May 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yim is ~~ON HOLD~~	+	==Structure of a Legionella effector==
-		+	<StructureSection load='5yim' size='340' side='right' caption='[[5yim]], [[Resolution\|resolution]] 3.39Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5yim]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YIM FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5yij\|5yij]], [[5yik\|5yik]]</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=5yim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yim OCA], [http://pdbe.org/5yim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yim RCSB], [http://www.ebi.ac.uk/pdbsum/5yim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yim ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dong, Y]]
		+	[[Category: Feng, Y]]
		+	[[Category: Wang, W]]
		+	[[Category: Monomer]]
		+	[[Category: Multi-domain protein]]
		+	[[Category: Transferase]]

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

OCA — Wed, 11 Oct 2017 05:25:15 GMT

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

←Older revision

Revision as of 05:25, 11 October 2017

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

OCA — Wed, 11 Oct 2017 05:25:14 GMT

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

New page

'''Unreleased structure'''

The entry 5yim is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]