4j5r - Revision history

OCA at 15:36, 20 September 2023

OCA — Wed, 20 Sep 2023 15:36:23 GMT

←Older revision		Revision as of 15:36, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4j5r]] is a 2 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=4J5R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J5R FirstGlance]. <br>		<table><tr><td colspan='2'>[[4j5r]] is a 2 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=4J5R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J5R FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1R:5-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE'>A1R</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 1.25Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1R:5-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE'>A1R</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=4j5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j5r OCA], [https://pdbe.org/4j5r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j5r RCSB], [https://www.ebi.ac.uk/pdbsum/4j5r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j5r 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=4j5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j5r OCA], [https://pdbe.org/4j5r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j5r RCSB], [https://www.ebi.ac.uk/pdbsum/4j5r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j5r ProSAT]</span></td></tr>
	</table>		</table>

OCA at 21:33, 16 November 2022

OCA — Wed, 16 Nov 2022 21:33:59 GMT

←Older revision		Revision as of 21:33, 16 November 2022
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	==TARG1 (C6orf130), Terminal ADP-ribose Glycohydrolase 1 bound to ADP-HPD==		==TARG1 (C6orf130), Terminal ADP-ribose Glycohydrolase 1 bound to ADP-HPD==
-	<StructureSection load='4j5r' size='340' side='right' caption='[[4j5r]], [[Resolution\|resolution]] 1.25Å' scene=''>	+	<StructureSection load='4j5r' size='340' side='right'caption='[[4j5r]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4j5r]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J5R OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4J5R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4j5r]] is a 2 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=4J5R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J5R FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A1R:5-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE'>A1R</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1R:5-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE'>A1R</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4j5q\|4j5q]], [[4j5s\|4j5s]]</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=4j5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j5r OCA], [https://pdbe.org/4j5r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j5r RCSB], [https://www.ebi.ac.uk/pdbsum/4j5r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j5r ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">OARD1, C6orf130 ([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=4j5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j5r OCA], [~~http~~://pdbe.org/4j5r PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4j5r RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4j5r PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4j5r ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/OARD1_HUMAN OARD1_HUMAN]] Deacetylates O-acetyl-ADP ribose, a signaling molecule generated by the deacetylation of acetylated lysine residues in histones and other proteins. Catalyzes the deacylation of O-acetyl-ADP-ribose, O-propionyl-ADP-ribose and O-butyryl-ADP-ribose, yielding ADP-ribose plus acetate, propionate and butyrate, respectively.	+	[https://www.uniprot.org/uniprot/OARD1_HUMAN OARD1_HUMAN] Deacetylates O-acetyl-ADP ribose, a signaling molecule generated by the deacetylation of acetylated lysine residues in histones and other proteins. Catalyzes the deacylation of O-acetyl-ADP-ribose, O-propionyl-ADP-ribose and O-butyryl-ADP-ribose, yielding ADP-ribose plus acetate, propionate and butyrate, respectively.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Appel, C D~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Krahn, J~~]]	+	[[Category: Appel CD]]
-	[[Category: ~~Schellenberg, M~~ J]]	+	[[Category: Krahn J]]
-	[[Category: ~~Williams, R S~~]]	+	[[Category: Schellenberg MJ]]
-	[[Category: ~~Adp-ribose]]~~	+	[[Category: Williams RS]]
-	~~[[Category: Cellular signaling]]~~	+
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Glycohydrolase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Macro domain]]~~	+
-	~~[[Category: Parp]]~~	+
-	~~[[Category: Poly-adp ribose~~]]	+

OCA at 21:52, 4 August 2016

OCA — Thu, 04 Aug 2016 21:52:09 GMT

←Older revision		Revision as of 21:52, 4 August 2016
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-	{{STRUCTURE_4j5r\| PDB=4j5r \| SCENE= }}
-	===TARG1 (C6orf130), Terminal ADP-ribose Glycohydrolase 1 bound to ADP-HPD===
-	{{ABSTRACT_PUBMED_23481255}}

-	==~~About this Structure~~==	+	==TARG1 (C6orf130), Terminal ADP-ribose Glycohydrolase 1 bound to ADP-HPD==
-	[[4j5r]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J5R OCA].	+	<StructureSection load='4j5r' size='340' side='right' caption='[[4j5r]], [[Resolution\|resolution]] 1.25Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4j5r]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J5R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4J5R FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A1R:5-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE'>A1R</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4j5q\|4j5q]], [[4j5s\|4j5s]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">OARD1, C6orf130 ([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=4j5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j5r OCA], [http://pdbe.org/4j5r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4j5r RCSB], [http://www.ebi.ac.uk/pdbsum/4j5r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4j5r ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/OARD1_HUMAN OARD1_HUMAN]] Deacetylates O-acetyl-ADP ribose, a signaling molecule generated by the deacetylation of acetylated lysine residues in histones and other proteins. Catalyzes the deacylation of O-acetyl-ADP-ribose, O-propionyl-ADP-ribose and O-butyryl-ADP-ribose, yielding ADP-ribose plus acetate, propionate and butyrate, respectively.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Adenosine diphosphate (ADP)-ribosylation is a post-translational protein modification implicated in the regulation of a range of cellular processes. A family of proteins that catalyse ADP-ribosylation reactions are the poly(ADP-ribose) (PAR) polymerases (PARPs). PARPs covalently attach an ADP-ribose nucleotide to target proteins and some PARP family members can subsequently add additional ADP-ribose units to generate a PAR chain. The hydrolysis of PAR chains is catalysed by PAR glycohydrolase (PARG). PARG is unable to cleave the mono(ADP-ribose) unit directly linked to the protein and although the enzymatic activity that catalyses this reaction has been detected in mammalian cell extracts, the protein(s) responsible remain unknown. Here, we report the homozygous mutation of the c6orf130 gene in patients with severe neurodegeneration, and identify C6orf130 as a PARP-interacting protein that removes mono(ADP-ribosyl)ation on glutamate amino acid residues in PARP-modified proteins. X-ray structures and biochemical analysis of C6orf130 suggest a mechanism of catalytic reversal involving a transient C6orf130 lysyl-(ADP-ribose) intermediate. Furthermore, depletion of C6orf130 protein in cells leads to proliferation and DNA repair defects. Collectively, our data suggest that C6orf130 enzymatic activity has a role in the turnover and recycling of protein ADP-ribosylation, and we have implicated the importance of this protein in supporting normal cellular function in humans.

-	~~==Reference==~~	+	Deficiency of terminal ADP-ribose protein glycohydrolase TARG1/C6orf130 in neurodegenerative disease.,Sharifi R, Morra R, Denise Appel C, Tallis M, Chioza B, Jankevicius G, Simpson MA, Matic I, Ozkan E, Golia B, Schellenberg MJ, Weston R, Williams JG, Rossi MN, Galehdari H, Krahn J, Wan A, Trembath RC, Crosby AH, Ahel D, Hay R, Ladurner AG, Timinszky G, Williams RS, Ahel I EMBO J. 2013 Mar 12. doi: 10.1038/emboj.2013.51. PMID:23481255<ref>PMID:23481255</ref>
-	<ref ~~group="xtra"~~>PMID:~~023481255~~</ref><~~references group~~="~~xtra~~"/><references/>	+
-	[[Category: ~~Homo sapiens~~]]	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: Appel, C D.]]	+	</div>
-	[[Category: Krahn, J.]]	+	<div class="pdbe-citations 4j5r" style="background-color:#fffaf0;"></div>
-	[[Category: Schellenberg, M J.]]	+	== References ==
-	[[Category: Williams, R S.]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Appel, C D]]
		+	[[Category: Krahn, J]]
		+	[[Category: Schellenberg, M J]]
		+	[[Category: Williams, R S]]
	[[Category: Adp-ribose]]		[[Category: Adp-ribose]]
	[[Category: Cellular signaling]]		[[Category: Cellular signaling]]

OCA at 12:41, 3 July 2013

OCA — Wed, 03 Jul 2013 12:41:55 GMT

←Older revision		Revision as of 12:41, 3 July 2013
Line 5:		Line 5:
	==About this Structure==		==About this Structure==
	[[4j5r]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J5R OCA].		[[4j5r]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J5R OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023481255</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Appel, C D.]]		[[Category: Appel, C D.]]

OCA at 08:51, 27 March 2013

OCA — Wed, 27 Mar 2013 08:51:42 GMT

←Older revision		Revision as of 08:51, 27 March 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4j5r\| PDB=4j5r \| SCENE= }}
		+	===TARG1 (C6orf130), Terminal ADP-ribose Glycohydrolase 1 bound to ADP-HPD===
		+	{{ABSTRACT_PUBMED_23481255}}

-	~~The entry~~ 4j5r is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[4j5r]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J5R OCA].
-	~~Authors~~: ~~Schellenberg, M~~.J., Appel, C.D., Krahn, J., Williams, R.S.	+	[[Category: Homo sapiens]]
-		+	[[Category: Appel, C D.]]
-	~~Description~~: ~~TARG1 (C6orf130), Terminal ADP~~-ribose Glycohydrolase ~~1 bound to ADP~~-~~HPD~~	+	[[Category: Krahn, J.]]
		+	[[Category: Schellenberg, M J.]]
		+	[[Category: Williams, R S.]]
		+	[[Category: Adp-ribose]]
		+	[[Category: Cellular signaling]]
		+	[[Category: Dna repair]]
		+	[[Category: Glycohydrolase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Macro domain]]
		+	[[Category: Parp]]
		+	[[Category: Poly-adp ribose]]

OCA at 13:49, 6 March 2013

OCA — Wed, 06 Mar 2013 13:49:24 GMT

←Older revision		Revision as of 13:49, 6 March 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4j5r is ON HOLD	+	The entry 4j5r is ON HOLD until Paper Publication

	Authors: Schellenberg, M.J., Appel, C.D., Krahn, J., Williams, R.S.		Authors: Schellenberg, M.J., Appel, C.D., Krahn, J., Williams, R.S.

	Description: TARG1 (C6orf130), Terminal ADP-ribose Glycohydrolase 1 bound to ADP-HPD		Description: TARG1 (C6orf130), Terminal ADP-ribose Glycohydrolase 1 bound to ADP-HPD

OCA: Protected "4j5r" [edit=sysop:move=sysop]

OCA — Wed, 20 Feb 2013 13:31:13 GMT

Protected "4j5r" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:31, 20 February 2013

OCA: New page: '''Unreleased structure''' The entry 4j5r is ON HOLD Authors: Schellenberg, M.J., Appel, C.D., Krahn, J., Williams, R.S. Description: TARG1 (C6orf130), Terminal ADP-ribose Glycohydrola...

OCA — Wed, 20 Feb 2013 13:31:12 GMT

New page: '''Unreleased structure''' The entry 4j5r is ON HOLD Authors: Schellenberg, M.J., Appel, C.D., Krahn, J., Williams, R.S. Description: TARG1 (C6orf130), Terminal ADP-ribose Glycohydrola...

New page

'''Unreleased structure'''

The entry 4j5r is ON HOLD

Authors: Schellenberg, M.J., Appel, C.D., Krahn, J., Williams, R.S.

Description: TARG1 (C6orf130), Terminal ADP-ribose Glycohydrolase 1 bound to ADP-HPD