7aqm - Revision history

OCA at 12:14, 1 February 2024

2024-02-01T12:14:26Z

←Older revision		Revision as of 12:14, 1 February 2024
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	<StructureSection load='7aqm' size='340' side='right'caption='[[7aqm]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='7aqm' size='340' side='right'caption='[[7aqm]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7aqm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Coelacanth Coelacanth~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7AQM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AQM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7aqm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Latimeria_chalumnae Latimeria chalumnae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7AQM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AQM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RVK:Adenosine+5-diphosphoric+acid+beta-[(3beta,4beta-dihydroxy-5beta-methoxytetrahydrofuran-2alpha-yl)methyl]+estere'>RVK</scene>~~</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]] 2.5Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADPRHL2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7897 Coelacanth])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RVK:Adenosine+5-diphosphoric+acid+beta-[(3beta,4beta-dihydroxy-5beta-methoxytetrahydrofuran-2alpha-yl)methyl]+estere'>RVK</scene></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=7aqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7aqm OCA], [https://pdbe.org/7aqm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7aqm RCSB], [https://www.ebi.ac.uk/pdbsum/7aqm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7aqm 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=7aqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7aqm OCA], [https://pdbe.org/7aqm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7aqm RCSB], [https://www.ebi.ac.uk/pdbsum/7aqm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7aqm ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ADPRS_LATCH ADPRS_LATCH] ADP-ribosylhydrolase that preferentially hydrolyzes the scissile alpha-O-linkage attached to the anomeric C1'' position of ADP-ribose and acts on different substrates, such as proteins ADP-ribosylated on serine and threonine, free poly(ADP-ribose) and O-acetyl-ADP-D-ribose (PubMed:30472116). Specifically acts as a serine mono-ADP-ribosylhydrolase by mediating the removal of mono-ADP-ribose attached to serine residues on proteins, thereby playing a key role in DNA damage response (PubMed:30472116). Serine ADP-ribosylation of proteins constitutes the primary form of ADP-ribosylation of proteins in response to DNA damage (By similarity). Does not hydrolyze ADP-ribosyl-arginine, -cysteine, -diphthamide, or -asparagine bonds (By similarity). Also able to degrade protein free poly(ADP-ribose), which is synthesized in response to DNA damage: free poly(ADP-ribose) acts as a potent cell death signal and its degradation by ADPRHL2 protects cells from poly(ADP-ribose)-dependent cell death, a process named parthanatos (PubMed:30472116). Also hydrolyzes free poly(ADP-ribose) in mitochondria (By similarity). Specifically digests O-acetyl-ADP-D-ribose, a product of deacetylation reactions catalyzed by sirtuins (By similarity). Specifically degrades 1''-O-acetyl-ADP-D-ribose isomer, rather than 2''-O-acetyl-ADP-D-ribose or 3''-O-acetyl-ADP-D-ribose isomers (By similarity).[UniProtKB:Q9NX46]<ref>PMID:30472116</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Coelacanth]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ahel, I]]
-	[[Category: Rack, J G.M]]
-	[[Category: Zorzini, V]]
-	[[Category: Adp-ribosylserine hydrolase]]
-	[[Category: Alpha-1''-o-methyl-adp ribose]]
-	[[Category: Arh3]]
-	[[Category: Hydrolase]]
	[[Category: Latimeria chalumnae]]		[[Category: Latimeria chalumnae]]
		+	[[Category: Ahel I]]
		+	[[Category: Rack JGM]]
		+	[[Category: Zorzini V]]

OCA at 05:49, 6 October 2021

2021-10-06T05:49:46Z

←Older revision		Revision as of 05:49, 6 October 2021
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	==ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in complex with alpha-1''-O-methyl-ADP-ribose (meADPr)==		==ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in complex with alpha-1''-O-methyl-ADP-ribose (meADPr)==
-	<StructureSection load='7aqm' size='340' side='right'caption='[[7aqm]]' scene=''>	+	<StructureSection load='7aqm' size='340' side='right'caption='[[7aqm]], [[Resolution\|resolution]] 2.50Å' 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=7AQM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AQM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7aqm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Coelacanth Coelacanth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7AQM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AQM 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=7aqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7aqm OCA], [https://pdbe.org/7aqm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7aqm RCSB], [https://www.ebi.ac.uk/pdbsum/7aqm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7aqm ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RVK:Adenosine+5-diphosphoric+acid+beta-[(3beta,4beta-dihydroxy-5beta-methoxytetrahydrofuran-2alpha-yl)methyl]+estere'>RVK</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADPRHL2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7897 Coelacanth])</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=7aqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7aqm OCA], [https://pdbe.org/7aqm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7aqm RCSB], [https://www.ebi.ac.uk/pdbsum/7aqm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7aqm ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Poly(ADP-ribosyl)ation (PAR) is a versatile and complex posttranslational modification composed of repeating units of ADP-ribose arranged into linear or branched polymers. This scaffold is linked to the regulation of many of cellular processes including the DNA damage response, alteration of chromatin structure and Wnt signalling. Despite decades of research, the principles and mechanisms underlying all steps of PAR removal remain actively studied. In this work, we synthesise well-defined PAR branch point molecules and demonstrate that PARG, but not ARH3, can resolve this distinct PAR architecture. Structural analysis of ARH3 in complex with dimeric ADP-ribose as well as an ADP-ribosylated peptide reveal the molecular basis for the hydrolysis of linear and terminal ADP-ribose linkages. We find that ARH3-dependent hydrolysis requires both rearrangement of a catalytic glutamate and induction of an unusual, square-pyramidal magnesium coordination geometry.
		+
		+	Mechanistic insights into the three steps of poly(ADP-ribosylation) reversal.,Rack JGM, Liu Q, Zorzini V, Voorneveld J, Ariza A, Honarmand Ebrahimi K, Reber JM, Krassnig SC, Ahel D, van der Marel GA, Mangerich A, McCullagh JSO, Filippov DV, Ahel I Nat Commun. 2021 Jul 28;12(1):4581. doi: 10.1038/s41467-021-24723-3. PMID:34321462<ref>PMID:34321462</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7aqm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Coelacanth]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ahel I]]	+	[[Category: Ahel, I]]
-	[[Category: Rack ~~JGM~~]]	+	[[Category: Rack, J G.M]]
-	[[Category: Zorzini V]]	+	[[Category: Zorzini, V]]
		+	[[Category: Adp-ribosylserine hydrolase]]
		+	[[Category: Alpha-1''-o-methyl-adp ribose]]
		+	[[Category: Arh3]]
		+	[[Category: Hydrolase]]
		+	[[Category: Latimeria chalumnae]]

OCA at 14:45, 17 June 2021

2021-06-17T14:45:16Z

←Older revision		Revision as of 14:45, 17 June 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7aqm is ~~ON HOLD until Paper Publication~~	+	==ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in complex with alpha-1''-O-methyl-ADP-ribose (meADPr)==
-		+	<StructureSection load='7aqm' size='340' side='right'caption='[[7aqm]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7AQM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AQM FirstGlance]. <br>
-	~~Description~~:	+	</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=7aqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7aqm OCA], [https://pdbe.org/7aqm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7aqm RCSB], [https://www.ebi.ac.uk/pdbsum/7aqm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7aqm ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Ahel I]]
		+	[[Category: Rack JGM]]
		+	[[Category: Zorzini V]]

OCA at 10:55, 16 December 2020

2020-12-16T10:55:53Z

←Older revision		Revision as of 10:55, 16 December 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

2020-10-28T18:58:34Z

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

←Older revision

Revision as of 18:58, 28 October 2020

OCA: New page: '''Unreleased structure''' The entry 7aqm is ON HOLD Authors: Description: Category: Unreleased Structures

2020-10-28T18:58:33Z

New page: '''Unreleased structure''' The entry 7aqm is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7aqm is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]