6p74 - Revision history

OCA at 14:54, 13 March 2024

2024-03-13T14:54:09Z

←Older revision		Revision as of 14:54, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6p74' size='340' side='right'caption='[[6p74]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6p74' size='340' side='right'caption='[[6p74]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6p74]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_51532 Atcc 51532~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P74 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6P74 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6p74]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_scotoductus Thermus scotoductus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P74 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6P74 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene>, <scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</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]] 2.2Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TSC_c04750 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37636 ATCC 51532])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene>, <scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</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=6p74 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p74 OCA], [~~http~~://pdbe.org/6p74 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6p74 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6p74 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6p74 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=6p74 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p74 OCA], [https://pdbe.org/6p74 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6p74 RCSB], [https://www.ebi.ac.uk/pdbsum/6p74 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6p74 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/OLD_THESS OLD_THESS] An exodeoxyribonuclease that degrades linear or supercoiled dsDNA from 5'-3'. Nicks and linearizes circular DNA. Activity is not stimulated by ATP or AMP-PNP, although it has DNA-stimulated ATPase activity.<ref>PMID:32009148</ref>
-	~~OLD family nucleases contain an N-terminal ATPase domain and a C-terminal Toprim domain. Homologs segregate into two classes based on primary sequence length and the presence~~/~~absence of a unique UvrD~~/~~PcrA/Rep-like helicase gene immediately downstream in the genome~~. Although we previously defined the catalytic machinery controlling Class 2 nuclease cleavage, degenerate conservation of the C-termini between classes precludes pinpointing the analogous residues in Class 1 enzymes by sequence alignment alone. ~~Our Class 2 structures also provide no information on ATPase domain architecture and ATP hydrolysis. Here we present the full~~-~~length structure of the Class 1 OLD nuclease from Thermus scotoductus (Ts) at 2~~.~~20 A resolution, which reveals a dimerization domain inserted into an N-terminal ABC ATPase fold~~ and a C-terminal Toprim domain. Structural homology with genome maintenance proteins identifies conserved residues responsible for Ts OLD ATPase activity. Ts OLD lacks the C-terminal helical domain present in Class 2 OLD homologs yet preserves the spatial organization of the nuclease active site, arguing that OLD proteins use a conserved catalytic mechanism for DNA ~~cleavage~~. ~~We also demonstrate that mutants perturbing~~ ATP ~~hydrolysis~~ or DNA ~~cleavage in vitro impair P2 OLD~~-~~mediated killing of recBC-Escherichia coli hosts, indicating that both the~~ ATPase ~~and nuclease activities are required for OLD function in vivo~~.	+
-		+
-	The full-length structure of Thermus scotoductus OLD defines the ATP hydrolysis properties and catalytic mechanism of Class 1 OLD family nucleases.,Schiltz CJ, Adams MC, Chappie JS Nucleic Acids Res. 2020 Feb 3. pii: 5721213. doi: 10.1093/nar/gkaa059. PMID:32009148<ref>PMID:32009148</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6p74" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 51532]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Chappie, J S~~]]	+	[[Category: Thermus scotoductus]]
-	[[Category: ~~Schiltz, C J~~]]	+	[[Category: Chappie JS]]
-	[[Category: ~~Abc atpase]]~~	+	[[Category: Schiltz CJ]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nuclease~~]]	+

OCA at 07:26, 19 February 2020

2020-02-19T07:26:44Z

←Older revision		Revision as of 07:26, 19 February 2020
Line 3:		Line 3:
	<StructureSection load='6p74' size='340' side='right'caption='[[6p74]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6p74' size='340' side='right'caption='[[6p74]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6p74]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P74 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P74 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6p74]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_51532 Atcc 51532]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P74 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P74 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene>, <scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene>, <scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TSC_c04750 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37636 ATCC 51532])</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=6p74 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p74 OCA], [http://pdbe.org/6p74 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p74 RCSB], [http://www.ebi.ac.uk/pdbsum/6p74 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p74 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=6p74 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p74 OCA], [http://pdbe.org/6p74 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p74 RCSB], [http://www.ebi.ac.uk/pdbsum/6p74 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p74 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	OLD family nucleases contain an N-terminal ATPase domain and a C-terminal Toprim domain. Homologs segregate into two classes based on primary sequence length and the presence/absence of a unique UvrD/PcrA/Rep-like helicase gene immediately downstream in the genome. Although we previously defined the catalytic machinery controlling Class 2 nuclease cleavage, degenerate conservation of the C-termini between classes precludes pinpointing the analogous residues in Class 1 enzymes by sequence alignment alone. Our Class 2 structures also provide no information on ATPase domain architecture and ATP hydrolysis. Here we present the full-length structure of the Class 1 OLD nuclease from Thermus scotoductus (Ts) at 2.20 A resolution, which reveals a dimerization domain inserted into an N-terminal ABC ATPase fold and a C-terminal Toprim domain. Structural homology with genome maintenance proteins identifies conserved residues responsible for Ts OLD ATPase activity. Ts OLD lacks the C-terminal helical domain present in Class 2 OLD homologs yet preserves the spatial organization of the nuclease active site, arguing that OLD proteins use a conserved catalytic mechanism for DNA cleavage. We also demonstrate that mutants perturbing ATP hydrolysis or DNA cleavage in vitro impair P2 OLD-mediated killing of recBC-Escherichia coli hosts, indicating that both the ATPase and nuclease activities are required for OLD function in vivo.
		+
		+	The full-length structure of Thermus scotoductus OLD defines the ATP hydrolysis properties and catalytic mechanism of Class 1 OLD family nucleases.,Schiltz CJ, Adams MC, Chappie JS Nucleic Acids Res. 2020 Feb 3. pii: 5721213. doi: 10.1093/nar/gkaa059. PMID:32009148<ref>PMID:32009148</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6p74" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 51532]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Chappie, J S]]		[[Category: Chappie, J S]]

OCA at 15:33, 29 January 2020

2020-01-29T15:33:30Z

←Older revision		Revision as of 15:33, 29 January 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6p74 ~~is ON HOLD~~	+	==OLD nuclease from Thermus Scotoductus==
-		+	<StructureSection load='6p74' size='340' side='right'caption='[[6p74]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6p74]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P74 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P74 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene>, <scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6p74 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p74 OCA], [http://pdbe.org/6p74 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p74 RCSB], [http://www.ebi.ac.uk/pdbsum/6p74 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p74 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Chappie, J S]]
		+	[[Category: Schiltz, C J]]
		+	[[Category: Abc atpase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nuclease]]

OCA: Protected "6p74" [edit=sysop:move=sysop]

2019-06-12T04:05:49Z

Protected "6p74" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:05, 12 June 2019

OCA: New page: '''Unreleased structure''' The entry 6p74 is ON HOLD Authors: Description: Category: Unreleased Structures

2019-06-12T04:05:47Z

New page: '''Unreleased structure''' The entry 6p74 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6p74 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]