5zdd - Revision history

OCA at 10:27, 27 March 2024

OCA — Wed, 27 Mar 2024 10:27:34 GMT

←Older revision		Revision as of 10:27, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5zdd' size='340' side='right'caption='[[5zdd]], [[Resolution\|resolution]] 2.73Å' scene=''>		<StructureSection load='5zdd' size='340' side='right'caption='[[5zdd]], [[Resolution\|resolution]] 2.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zdd]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Deira Deira~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZDD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZDD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zdd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZDD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZDD 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=PO4:PHOSPHATE+ION'>PO4</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]] 2.725Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DR_B0099 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243230 DEIRA])~~</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=PO4:PHOSPHATE+ION'>PO4</scene></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=5zdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zdd OCA], [~~http~~://pdbe.org/5zdd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zdd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zdd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zdd 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=5zdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zdd OCA], [https://pdbe.org/5zdd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zdd RCSB], [https://www.ebi.ac.uk/pdbsum/5zdd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zdd ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q9RZM4_DEIRA Q9RZM4_DEIRA]
-	Poly-ADP-ribosylation, a post-translational modification involved in various cellular processes, is well characterized in eukaryotes but thought to be devoid in bacteria. Here, we solve crystal structures of ADP-ribose-bound poly(ADP-ribose)glycohydrolase from the radioresistant bacterium Deinococcus radiodurans (DrPARG), revealing a solvent-accessible 2'-hydroxy group of ADP-ribose, which suggests that DrPARG may possess endo-glycohydrolase activity toward poly-ADP-ribose (PAR). We confirm the existence of PAR in D. radiodurans and show that disruption of DrPARG expression causes accumulation of endogenous PAR and compromises recovery from UV radiation damage. Moreover, endogenous PAR levels in D. radiodurans are elevated after UV irradiation, indicating that PARylation may be involved in resistance to genotoxic stresses. These findings provide structural insights into a bacterial-type PARG and suggest the existence of a prokaryotic PARylation machinery that may be involved in stress responses.	+
-		+
-	~~Structural and biochemical evidence supporting poly ADP-ribosylation in the bacterium Deinococcus radiodurans.,Cho CC, Chien CY, Chiu YC, Lin MH, Hsu CH Nat Commun. 2019 Apr 2;10(1)~~:~~1491. doi: 10.1038~~/~~s41467-019-09153-6. PMID:30940816<ref>PMID:30940816<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5zdd" style="background-color:#fffaf0;"><~~/~~div>~~	+

	==See Also==		==See Also==
	*[[Poly(ADP-ribose) glycohydrolase 3D structures\|Poly(ADP-ribose) glycohydrolase 3D structures]]		*[[Poly(ADP-ribose) glycohydrolase 3D structures\|Poly(ADP-ribose) glycohydrolase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Deira~~]]	+	[[Category: Deinococcus radiodurans R1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cho~~, C C~~]]	+	[[Category: Cho CC]]
-	[[Category: Hsu~~, C H]]~~	+	[[Category: Hsu CH]]
-	~~[[Category: Adp-ribose]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:48, 11 March 2020

OCA — Wed, 11 Mar 2020 07:48:52 GMT

←Older revision		Revision as of 07:48, 11 March 2020
Line 1:		Line 1:

	==Crystal structure of poly(ADP-ribose) glycohydrolase (PARG) from Deinococcus radiodurans in complex with ADP-ribose (P212121)==		==Crystal structure of poly(ADP-ribose) glycohydrolase (PARG) from Deinococcus radiodurans in complex with ADP-ribose (P212121)==
-	<StructureSection load='5zdd' size='340' side='right' caption='[[5zdd]], [[Resolution\|resolution]] 2.73Å' scene=''>	+	<StructureSection load='5zdd' size='340' side='right'caption='[[5zdd]], [[Resolution\|resolution]] 2.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zdd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZDD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZDD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zdd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Deira Deira]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZDD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZDD 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=PO4:PHOSPHATE+ION'>PO4</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=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DR_B0099 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243230 DEIRA])</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=5zdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zdd OCA], [http://pdbe.org/5zdd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zdd RCSB], [http://www.ebi.ac.uk/pdbsum/5zdd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zdd 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=5zdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zdd OCA], [http://pdbe.org/5zdd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zdd RCSB], [http://www.ebi.ac.uk/pdbsum/5zdd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zdd ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Poly-ADP-ribosylation, a post-translational modification involved in various cellular processes, is well characterized in eukaryotes but thought to be devoid in bacteria. Here, we solve crystal structures of ADP-ribose-bound poly(ADP-ribose)glycohydrolase from the radioresistant bacterium Deinococcus radiodurans (DrPARG), revealing a solvent-accessible 2'-hydroxy group of ADP-ribose, which suggests that DrPARG may possess endo-glycohydrolase activity toward poly-ADP-ribose (PAR). We confirm the existence of PAR in D. radiodurans and show that disruption of DrPARG expression causes accumulation of endogenous PAR and compromises recovery from UV radiation damage. Moreover, endogenous PAR levels in D. radiodurans are elevated after UV irradiation, indicating that PARylation may be involved in resistance to genotoxic stresses. These findings provide structural insights into a bacterial-type PARG and suggest the existence of a prokaryotic PARylation machinery that may be involved in stress responses.
		+
		+	Structural and biochemical evidence supporting poly ADP-ribosylation in the bacterium Deinococcus radiodurans.,Cho CC, Chien CY, Chiu YC, Lin MH, Hsu CH Nat Commun. 2019 Apr 2;10(1):1491. doi: 10.1038/s41467-019-09153-6. PMID:30940816<ref>PMID:30940816</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5zdd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Poly(ADP-ribose) glycohydrolase 3D structures\|Poly(ADP-ribose) glycohydrolase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Deira]]
		+	[[Category: Large Structures]]
	[[Category: Cho, C C]]		[[Category: Cho, C C]]
	[[Category: Hsu, C H]]		[[Category: Hsu, C H]]
	[[Category: Adp-ribose]]		[[Category: Adp-ribose]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 15:11, 27 February 2019

OCA — Wed, 27 Feb 2019 15:11:48 GMT

←Older revision		Revision as of 15:11, 27 February 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5zdd is ON HOLD until Paper Publication~~	+	==Crystal structure of poly(ADP-ribose) glycohydrolase (PARG) from Deinococcus radiodurans in complex with ADP-ribose (P212121)==
-		+	<StructureSection load='5zdd' size='340' side='right' caption='[[5zdd]], [[Resolution\|resolution]] 2.73Å' scene=''>
-	~~Authors: Cho, C.C., Hsu, C.H.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5zdd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZDD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZDD FirstGlance]. <br>
-	~~Description:~~ Crystal structure of poly(ADP-ribose) glycohydrolase (PARG) from Deinococcus radiodurans in complex with ADP-ribose (P212121)	+	</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=PO4:PHOSPHATE+ION'>PO4</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=5zdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zdd OCA], [http://pdbe.org/5zdd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zdd RCSB], [http://www.ebi.ac.uk/pdbsum/5zdd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zdd ProSAT]</span></td></tr>
-	[[Category: Cho, C.C]]	+	</table>
-	[[Category: Hsu, C.H]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Cho, C C]]
		+	[[Category: Hsu, C H]]
		+	[[Category: Adp-ribose]]
		+	[[Category: Hydrolase]]

OCA at 05:56, 21 March 2018

OCA — Wed, 21 Mar 2018 05:56:51 GMT

←Older revision		Revision as of 05:56, 21 March 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Cho, C.C., Hsu, C.H.		Authors: Cho, C.C., Hsu, C.H.

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

OCA — Wed, 28 Feb 2018 04:55:59 GMT

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

←Older revision

Revision as of 04:55, 28 February 2018

OCA: New page: '''Unreleased structure''' The entry 5zdd is ON HOLD Authors: Cho, C.C., Hsu, C.H. Description: Crystal structure of poly(ADP-ribose) glycohydrolase (PARG) from Deinococcus radiodurans...

OCA — Wed, 28 Feb 2018 04:55:58 GMT

New page: '''Unreleased structure''' The entry 5zdd is ON HOLD Authors: Cho, C.C., Hsu, C.H. Description: Crystal structure of poly(ADP-ribose) glycohydrolase (PARG) from Deinococcus radiodurans...

New page

'''Unreleased structure'''

The entry 5zdd is ON HOLD

Authors: Cho, C.C., Hsu, C.H.

Description: Crystal structure of poly(ADP-ribose) glycohydrolase (PARG) from Deinococcus radiodurans in complex with ADP-ribose (P212121)
[[Category: Unreleased Structures]]
[[Category: Cho, C.C]]
[[Category: Hsu, C.H]]