6b7o - Revision history

OCA at 10:15, 1 January 2020

OCA — Wed, 01 Jan 2020 10:15:02 GMT

←Older revision		Revision as of 10:15, 1 January 2020
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	==Crystal structure of Legionella effector sdeD (lpg2509) H67A in complex with ADP-ribosylated Ubiquitin==		==Crystal structure of Legionella effector sdeD (lpg2509) H67A in complex with ADP-ribosylated Ubiquitin==
-	<StructureSection load='6b7o' size='340' side='right' caption='[[6b7o]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='6b7o' size='340' side='right'caption='[[6b7o]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6b7o]] 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=6B7O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B7O FirstGlance]. <br>		<table><tr><td colspan='2'>[[6b7o]] 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=6B7O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B7O FirstGlance]. <br>
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	[[Category: Atcc 33152]]		[[Category: Atcc 33152]]
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Akturk, A]]		[[Category: Akturk, A]]
	[[Category: Mao, Y]]		[[Category: Mao, Y]]

OCA at 08:09, 14 June 2018

OCA — Thu, 14 Jun 2018 08:09:11 GMT

←Older revision		Revision as of 08:09, 14 June 2018
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/UBC_HUMAN UBC_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/UBC_HUMAN UBC_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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ubiquitination is a post-translational modification that regulates many cellular processes in eukaryotes(1-4). The conventional ubiquitination cascade culminates in a covalent linkage between the C terminus of ubiquitin (Ub) and a target protein, usually on a lysine side chain(1,5). Recent studies of the Legionella pneumophila SidE family of effector proteins revealed a ubiquitination method in which a phosphoribosyl ubiquitin (PR-Ub) is conjugated to a serine residue on substrates via a phosphodiester bond(6-8). Here we present the crystal structure of a fragment of the SidE family member SdeA that retains ubiquitination activity, and determine the mechanism of this unique post-translational modification. The structure reveals that the catalytic module contains two distinct functional units: a phosphodiesterase domain and a mono-ADP-ribosyltransferase domain. Biochemical analysis shows that the mono-ADP-ribosyltransferase domain-mediated conversion of Ub to ADP-ribosylated Ub (ADPR-Ub) and the phosphodiesterase domain-mediated ligation of PR-Ub to substrates are two independent activities of SdeA. Furthermore, we present two crystal structures of a homologous phosphodiesterase domain from the SidE family member SdeD (9) in complexes with Ub and ADPR-Ub. The structures suggest a mechanism for how SdeA processes ADPR-Ub to PR-Ub and AMP, and conjugates PR-Ub to a serine residue in substrates. Our study establishes the molecular mechanism of phosphoribosyl-linked ubiquitination and will enable future studies of this unusual type of ubiquitination in eukaryotes.
		+
		+	Mechanism of phosphoribosyl-ubiquitination mediated by a single Legionella effector.,Akturk A, Wasilko DJ, Wu X, Liu Y, Zhang Y, Qiu J, Luo ZQ, Reiter KH, Brzovic PS, Klevit RE, Mao Y Nature. 2018 May;557(7707):729-733. doi: 10.1038/s41586-018-0147-6. Epub 2018 May, 23. PMID:29795346<ref>PMID:29795346</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6b7o" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:18, 6 June 2018

OCA — Wed, 06 Jun 2018 06:18:14 GMT

←Older revision		Revision as of 06:18, 6 June 2018
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	<StructureSection load='6b7o' size='340' side='right' caption='[[6b7o]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='6b7o' size='340' side='right' caption='[[6b7o]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6b7o]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B7O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B7O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6b7o]] 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=6B7O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B7O FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AR6:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AR6</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AR6:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AR6</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lpg2509 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=446 ATCC 33152]), UBC ([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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6b7o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b7o OCA], [http://pdbe.org/6b7o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b7o RCSB], [http://www.ebi.ac.uk/pdbsum/6b7o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b7o 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=6b7o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b7o OCA], [http://pdbe.org/6b7o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b7o RCSB], [http://www.ebi.ac.uk/pdbsum/6b7o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b7o ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 33152]]
		+	[[Category: Human]]
	[[Category: Akturk, A]]		[[Category: Akturk, A]]
	[[Category: Mao, Y]]		[[Category: Mao, Y]]

OCA at 05:43, 18 April 2018

OCA — Wed, 18 Apr 2018 05:43:51 GMT

←Older revision		Revision as of 05:43, 18 April 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6b7o is ON HOLD until Paper Publication~~	+	==Crystal structure of Legionella effector sdeD (lpg2509) H67A in complex with ADP-ribosylated Ubiquitin==
-		+	<StructureSection load='6b7o' size='340' side='right' caption='[[6b7o]], [[Resolution\|resolution]] 1.85Å' scene=''>
-	~~Authors: Mao, Y., Akturk, A., Wasilko, J.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6b7o]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B7O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B7O FirstGlance]. <br>
-	~~Description:~~ Crystal structure of Legionella effector sdeD (lpg2509) H67A in complex with ADP-ribosylated Ubiquitin	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AR6:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AR6</scene></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=6b7o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b7o OCA], [http://pdbe.org/6b7o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b7o RCSB], [http://www.ebi.ac.uk/pdbsum/6b7o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b7o ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/UBC_HUMAN UBC_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: Akturk, A]]		[[Category: Akturk, A]]
		+	[[Category: Mao, Y]]
	[[Category: Wasilko, J]]		[[Category: Wasilko, J]]
-	[[Category: ~~Mao, Y~~]]	+	[[Category: Adpr-ub]]
		+	[[Category: Cell invasion]]
		+	[[Category: Legionella]]
		+	[[Category: Phosphodiesterase]]
		+	[[Category: Pr-ub]]
		+	[[Category: Sded]]
		+	[[Category: Ubiquitin]]

OCA at 04:55, 20 December 2017

OCA — Wed, 20 Dec 2017 04:55:31 GMT

←Older revision		Revision as of 04:55, 20 December 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6b7o is ON HOLD	+	The entry 6b7o is ON HOLD until Paper Publication

	Authors: Mao, Y., Akturk, A., Wasilko, J.		Authors: Mao, Y., Akturk, A., Wasilko, J.
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Akturk, A]]		[[Category: Akturk, A]]
-	[[Category: Mao, Y]]
	[[Category: Wasilko, J]]		[[Category: Wasilko, J]]
		+	[[Category: Mao, Y]]

OCA: Protected "6b7o" [edit=sysop:move=sysop]

OCA — Wed, 11 Oct 2017 05:38:41 GMT

Protected "6b7o" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:38, 11 October 2017

OCA: New page: '''Unreleased structure''' The entry 6b7o is ON HOLD Authors: Mao, Y., Akturk, A., Wasilko, J. Description: Crystal structure of Legionella effector sdeD (lpg2509) H67A in complex with...

OCA — Wed, 11 Oct 2017 05:38:40 GMT

New page: '''Unreleased structure''' The entry 6b7o is ON HOLD Authors: Mao, Y., Akturk, A., Wasilko, J. Description: Crystal structure of Legionella effector sdeD (lpg2509) H67A in complex with...

New page

'''Unreleased structure'''

The entry 6b7o is ON HOLD

Authors: Mao, Y., Akturk, A., Wasilko, J.

Description: Crystal structure of Legionella effector sdeD (lpg2509) H67A in complex with ADP-ribosylated Ubiquitin
[[Category: Unreleased Structures]]
[[Category: Akturk, A]]
[[Category: Mao, Y]]
[[Category: Wasilko, J]]