5zqy - Revision history

OCA at 09:04, 22 November 2023

OCA — Wed, 22 Nov 2023 09:04:18 GMT

←Older revision		Revision as of 09:04, 22 November 2023
Line 1:		Line 1:

	==Crystal structure of a poly(ADP-ribose) glycohydrolase==		==Crystal structure of a poly(ADP-ribose) glycohydrolase==
-	<StructureSection load='5zqy' size='340' side='right' caption='[[5zqy]], [[Resolution\|resolution]] 1.58Å' scene=''>	+	<StructureSection load='5zqy' size='340' side='right'caption='[[5zqy]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zqy]] is a 1 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=5ZQY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZQY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zqy]] is a 1 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=5ZQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZQY 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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.577Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADPRHL2, ARH3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Poly(ADP-ribose)_glycohydrolase Poly(ADP-ribose) glycohydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.143 3.2.1.143] </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=5zqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zqy OCA], [https://pdbe.org/5zqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zqy RCSB], [https://www.ebi.ac.uk/pdbsum/5zqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zqy 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=5zqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zqy OCA], [~~http~~://pdbe.org/5zqy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zqy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zqy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zqy ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Disease ==
		+	[https://www.uniprot.org/uniprot/ADPRS_HUMAN ADPRS_HUMAN] The disease is caused by variants affecting the gene represented in this entry.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~ARHL2_HUMAN ARHL2_HUMAN~~]~~] Poly(~~ADP-ribose~~) synthesized after DNA damage is only present transiently~~ and ~~is rapidly degraded by~~ poly(ADP-ribose) ~~glycohydrolase. Poly(~~ADP-ribose) ~~metabolism may be required for maintenance of the normal function of neuronal cells~~. ~~Generates~~ ADP-~~ribose from poly~~-(ADP-ribose), ~~but does~~ not hydrolyze ADP-~~ribose~~-arginine, -cysteine, -diphthamide, or -asparagine bonds. ~~Due~~ to ~~catalytic inactivity of PARG mitochondrial isoforms~~, ~~ARH3~~ is ~~the only PAR hydrolyzing enzyme~~ in mitochondria.<ref>PMID:16278211</ref>	+	[https://www.uniprot.org/uniprot/ADPRS_HUMAN ADPRS_HUMAN] ADP-ribose glycohydrolase 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, free poly(ADP-ribose) and O-acetyl-ADP-D-ribose (PubMed:21498885, PubMed:30045870, PubMed:29907568, PubMed:30401461, PubMed:33186521). 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:28650317, PubMed:29234005, PubMed:30045870, PubMed:33186521). Serine ADP-ribosylation of proteins constitutes the primary form of ADP-ribosylation of proteins in response to DNA damage (PubMed:29480802, PubMed:33186521). Does not hydrolyze ADP-ribosyl-arginine, -cysteine, -diphthamide, or -asparagine bonds (PubMed:16278211). 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:16278211). Also hydrolyzes free poly(ADP-ribose) in mitochondria (PubMed:22433848). Specifically digests O-acetyl-ADP-D-ribose, a product of deacetylation reactions catalyzed by sirtuins (PubMed:17075046, PubMed:21498885). 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 (PubMed:21498885).<ref>PMID:16278211</ref> <ref>PMID:17075046</ref> <ref>PMID:21498885</ref> <ref>PMID:22433848</ref> <ref>PMID:28650317</ref> <ref>PMID:29234005</ref> <ref>PMID:29480802</ref> <ref>PMID:29907568</ref> <ref>PMID:30045870</ref> <ref>PMID:30401461</ref> <ref>PMID:33186521</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:

	==See Also==		==See Also==
-	*[[Poly (ADP-ribose) glycohydrolase\|Poly (ADP-ribose) glycohydrolase]]	+	*[[Poly(ADP-ribose) glycohydrolase 3D structures\|Poly(ADP-ribose) glycohydrolase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: Liu, X]]	+	[[Category: Large Structures]]
-	[[Category: Ma, Y]]	+	[[Category: Liu X]]
-	[[Category: Wang, J]]	+	[[Category: Ma Y]]
-	[[Category: Wang, M]]	+	[[Category: Wang J]]
-	[[Category: Yuan, Z]]	+	[[Category: Wang M]]
-	~~[[Category: Hydrolase]]~~	+	[[Category: Yuan Z]]
-	~~[[Category: Lyase~~]]	+

OCA at 08:36, 26 September 2018

OCA — Wed, 26 Sep 2018 08:36:33 GMT

←Older revision		Revision as of 08:36, 26 September 2018
Line 3:		Line 3:
	<StructureSection load='5zqy' size='340' side='right' caption='[[5zqy]], [[Resolution\|resolution]] 1.58Å' scene=''>		<StructureSection load='5zqy' size='340' side='right' caption='[[5zqy]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zqy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZQY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zqy]] is a 1 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=5ZQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZQY 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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADPRHL2, ARH3 ([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/Poly(ADP-ribose)_glycohydrolase Poly(ADP-ribose) glycohydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.143 3.2.1.143] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Poly(ADP-ribose)_glycohydrolase Poly(ADP-ribose) glycohydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.143 3.2.1.143] </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=5zqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zqy OCA], [http://pdbe.org/5zqy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zqy RCSB], [http://www.ebi.ac.uk/pdbsum/5zqy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zqy 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=5zqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zqy OCA], [http://pdbe.org/5zqy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zqy RCSB], [http://www.ebi.ac.uk/pdbsum/5zqy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zqy ProSAT]</span></td></tr>
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5zqy" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5zqy" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Poly (ADP-ribose) glycohydrolase\|Poly (ADP-ribose) glycohydrolase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Liu, X]]		[[Category: Liu, X]]
	[[Category: Ma, Y]]		[[Category: Ma, Y]]

OCA at 16:09, 15 August 2018

OCA — Wed, 15 Aug 2018 16:09:26 GMT

←Older revision		Revision as of 16:09, 15 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zqy is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of a poly(ADP-ribose) glycohydrolase==
		+	<StructureSection load='5zqy' size='340' side='right' caption='[[5zqy]], [[Resolution\|resolution]] 1.58Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5zqy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZQY 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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Poly(ADP-ribose)_glycohydrolase Poly(ADP-ribose) glycohydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.143 3.2.1.143] </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=5zqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zqy OCA], [http://pdbe.org/5zqy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zqy RCSB], [http://www.ebi.ac.uk/pdbsum/5zqy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zqy ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ARHL2_HUMAN ARHL2_HUMAN]] Poly(ADP-ribose) synthesized after DNA damage is only present transiently and is rapidly degraded by poly(ADP-ribose) glycohydrolase. Poly(ADP-ribose) metabolism may be required for maintenance of the normal function of neuronal cells. Generates ADP-ribose from poly-(ADP-ribose), but does not hydrolyze ADP-ribose-arginine, -cysteine, -diphthamide, or -asparagine bonds. Due to catalytic inactivity of PARG mitochondrial isoforms, ARH3 is the only PAR hydrolyzing enzyme in mitochondria.<ref>PMID:16278211</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	ADP-ribosylation of proteins plays key roles in multiple biological processes, including DNA damage repair. Recent evidence suggests that serine is an important acceptor for ADP-ribosylation, and that serine ADP-ribosylation is hydrolyzed by ADP-ribosylhydrolase 3 (ARH3 or ADPRHL2). However, the structural details in ARH3-mediated hydrolysis remain elusive. Here, we determined the structure of ARH3 in a complex with ADP-ribose (ADPR). Our analyses revealed a group of acidic residues in ARH3 that keep two Mg2+ ions at the catalytic center for hydrolysis of Ser-linked ADP-ribosyl group. In particular, dynamic conformational changes involving Glu41 were observed in the catalytic center. Our observations suggest that Mg2+ ions together with Glu41 and water351 are likely to mediate the cleavage of the glycosidic bond in the serine-ADPR substrate. Moreover, we found that ADPR is buried in a groove and forms multiple hydrogen bonds with the main chain and side chains of ARH3 residues. On the basis of these structural findings, we used site -directed mutagenesis to examine the functional roles of key residues in the catalytic pocket of ARH3 in mediating the hydrolysis of ADP-ribosyl from serine and DNA damage repair. Moreover, we noted that ADPR recognition is essential for the recruitment of ARH3 to DNA lesions. Taken together, our study provides structural and functional insights into the molecular mechanism by which ARH3 hydrolyzes ADP-ribosyl group from serine and contributes to DNA damage repair.

-	~~Authors: Wang~~, M., Yuan, Z., Ma, Y~~., Wang, J.~~, Liu, X.	+	Structure-function analyses reveal the mechanism of the ARH3-dependent hydrolysis of ADP-ribosylation.,Wang M, Yuan Z, Xie R, Ma Y, Liu X, Yu X J Biol Chem. 2018 Jul 25. pii: RA118.004284. doi: 10.1074/jbc.RA118.004284. PMID:30045870<ref>PMID:30045870</ref>

-	~~Description: Crystal structure of~~ a ~~poly(ADP-ribose) glycohydrolase~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Wang, M]]~~	+	<div class="pdbe-citations 5zqy" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Liu, X]]		[[Category: Liu, X]]
-	[[Category: Yuan, Z]]
	[[Category: Ma, Y]]		[[Category: Ma, Y]]
	[[Category: Wang, J]]		[[Category: Wang, J]]
		+	[[Category: Wang, M]]
		+	[[Category: Yuan, Z]]
		+	[[Category: Hydrolase]]
		+	[[Category: Lyase]]

OCA at 04:43, 9 May 2018

OCA — Wed, 09 May 2018 04:43:36 GMT

←Older revision		Revision as of 04:43, 9 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zqy is ON HOLD	+	The entry 5zqy is ON HOLD until Paper Publication

	Authors: Wang, M., Yuan, Z., Ma, Y., Wang, J., Liu, X.		Authors: Wang, M., Yuan, Z., Ma, Y., Wang, J., Liu, X.

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

OCA — Wed, 25 Apr 2018 03:56:54 GMT

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

←Older revision

Revision as of 03:56, 25 April 2018

OCA: New page: '''Unreleased structure''' The entry 5zqy is ON HOLD Authors: Wang, M., Yuan, Z., Ma, Y., Wang, J., Liu, X. Description: Crystal structure of a poly(ADP-ribose) glycohydrolase [[Catego...

OCA — Wed, 25 Apr 2018 03:56:53 GMT

New page: '''Unreleased structure''' The entry 5zqy is ON HOLD Authors: Wang, M., Yuan, Z., Ma, Y., Wang, J., Liu, X. Description: Crystal structure of a poly(ADP-ribose) glycohydrolase [[Catego...

New page

'''Unreleased structure'''

The entry 5zqy is ON HOLD

Authors: Wang, M., Yuan, Z., Ma, Y., Wang, J., Liu, X.

Description: Crystal structure of a poly(ADP-ribose) glycohydrolase
[[Category: Unreleased Structures]]
[[Category: Wang, M]]
[[Category: Liu, X]]
[[Category: Yuan, Z]]
[[Category: Ma, Y]]
[[Category: Wang, J]]