5zo4 - Revision history

OCA at 10:28, 27 March 2024

2024-03-27T10:28:40Z

←Older revision		Revision as of 10:28, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5zo4' size='340' side='right'caption='[[5zo4]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5zo4' size='340' side='right'caption='[[5zo4]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zo4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZO4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZO4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zo4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_fabrum_str._J-07 Agrobacterium fabrum str. J-07]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZO4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZO4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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='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=5zo4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zo4 OCA], [~~http~~://pdbe.org/5zo4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zo4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zo4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zo4 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5zo4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zo4 OCA], [https://pdbe.org/5zo4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zo4 RCSB], [https://www.ebi.ac.uk/pdbsum/5zo4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zo4 ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	NrnC from Agrobacterium tumefaciens (At_NrnC, UniProt accession number A9CG28) is a nuclease containing a single DEDDy domain. Here, we determined the structures of both the apo and metal-ion-bound forms of At_NrnC. Although the overall structure of the At_NrnC protomer is similar to that of the RNase D exonuclease domain, nuclease assays unexpectedly revealed that At_NrnC possesses remarkably different substrate specificity. In contrast to RNase D, which degrades both single-stranded RNA (ssRNA) and double-stranded RNA (dsRNA), At_NrnC hydrolyses ssRNA, single-stranded DNA (ssDNA), and double-stranded DNA (dsDNA) with high efficiency but does not degrade dsRNA. Crystal packing analysis and biochemical data indicated that At_NrnC forms an octameric hollow cylindrical structure that allows ssRNA, ssDNA, and dsDNA, but not dsRNA, to enter the central tunnel where the multiple active sites perform hydrolysis. This novel structural feature confers a high processivity and is responsible for the preference of At_NrnC for longer dsDNA substrates.
-
-	NrnC, an RNase D-Like Protein From Agrobacterium, Is a Novel Octameric Nuclease That Specifically Degrades dsDNA but Leaves dsRNA Intact.,Yuan Z, Gao F, Yin K, Gu L Front Microbiol. 2019 Jan 7;9:3230. doi: 10.3389/fmicb.2018.03230. eCollection, 2018. PMID:30666241<ref>PMID:30666241</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5zo4" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Agrobacterium fabrum str. J-07]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gu~~, L C~~]]	+	[[Category: Gu LC]]
-	[[Category: Yuan~~, Z L]]~~	+	[[Category: Yuan ZL]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nuclease~~]]	+

OCA at 07:06, 10 April 2019

2019-04-10T07:06:08Z

←Older revision		Revision as of 07:06, 10 April 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 5zo4 is ~~ON HOLD until Paper~~ Publication	+	==inactive state of the nuclease==
		+	<StructureSection load='5zo4' size='340' side='right'caption='[[5zo4]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5zo4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZO4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZO4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5zo4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zo4 OCA], [http://pdbe.org/5zo4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zo4 RCSB], [http://www.ebi.ac.uk/pdbsum/5zo4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zo4 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	NrnC from Agrobacterium tumefaciens (At_NrnC, UniProt accession number A9CG28) is a nuclease containing a single DEDDy domain. Here, we determined the structures of both the apo and metal-ion-bound forms of At_NrnC. Although the overall structure of the At_NrnC protomer is similar to that of the RNase D exonuclease domain, nuclease assays unexpectedly revealed that At_NrnC possesses remarkably different substrate specificity. In contrast to RNase D, which degrades both single-stranded RNA (ssRNA) and double-stranded RNA (dsRNA), At_NrnC hydrolyses ssRNA, single-stranded DNA (ssDNA), and double-stranded DNA (dsDNA) with high efficiency but does not degrade dsRNA. Crystal packing analysis and biochemical data indicated that At_NrnC forms an octameric hollow cylindrical structure that allows ssRNA, ssDNA, and dsDNA, but not dsRNA, to enter the central tunnel where the multiple active sites perform hydrolysis. This novel structural feature confers a high processivity and is responsible for the preference of At_NrnC for longer dsDNA substrates.

-	~~Authors: Yuan~~, ~~Z.L~~., Gu, L.C.	+	NrnC, an RNase D-Like Protein From Agrobacterium, Is a Novel Octameric Nuclease That Specifically Degrades dsDNA but Leaves dsRNA Intact.,Yuan Z, Gao F, Yin K, Gu L Front Microbiol. 2019 Jan 7;9:3230. doi: 10.3389/fmicb.2018.03230. eCollection, 2018. PMID:30666241<ref>PMID:30666241</ref>

-	~~Description: inactive state~~ of the ~~nuclease~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Gu, L.C]]	+	<div class="pdbe-citations 5zo4" style="background-color:#fffaf0;"></div>
-	[[Category: Yuan, Z.L]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Gu, L C]]
		+	[[Category: Yuan, Z L]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nuclease]]

OCA at 05:47, 23 May 2018

2018-05-23T05:47:55Z

←Older revision		Revision as of 05:47, 23 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zo4 is ON HOLD	+	The entry 5zo4 is ON HOLD until Paper Publication

	Authors: Yuan, Z.L., Gu, L.C.		Authors: Yuan, Z.L., Gu, L.C.
Line 7:		Line 7:
	Description: inactive state of the nuclease		Description: inactive state of the nuclease
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Yuan, Z.L]]
	[[Category: Gu, L.C]]		[[Category: Gu, L.C]]
		+	[[Category: Yuan, Z.L]]

OCA: Protected "5zo4" [edit=sysop:move=sysop]

2018-04-18T04:07:08Z

Protected "5zo4" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:07, 18 April 2018

OCA: New page: '''Unreleased structure''' The entry 5zo4 is ON HOLD Authors: Yuan, Z.L., Gu, L.C. Description: inactive state of the nuclease Category: Unreleased Structures [[Category: Yuan, Z.L...

2018-04-18T04:07:07Z

New page: '''Unreleased structure''' The entry 5zo4 is ON HOLD Authors: Yuan, Z.L., Gu, L.C. Description: inactive state of the nuclease Category: Unreleased Structures [[Category: Yuan, Z.L...

New page

'''Unreleased structure'''

The entry 5zo4 is ON HOLD

Authors: Yuan, Z.L., Gu, L.C.

Description: inactive state of the nuclease
[[Category: Unreleased Structures]]
[[Category: Yuan, Z.L]]
[[Category: Gu, L.C]]