5dmp - Revision history

OCA at 21:50, 28 June 2023

2023-06-28T21:50:13Z

←Older revision		Revision as of 21:50, 28 June 2023
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	<StructureSection load='5dmp' size='340' side='right'caption='[[5dmp]], [[Resolution\|resolution]] 1.79Å' scene=''>		<StructureSection load='5dmp' size='340' side='right'caption='[[5dmp]], [[Resolution\|resolution]] 1.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dmp]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Dsm_17711 Dsm 17711~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DMP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5DMP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dmp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocella_paludicola Methanocella paludicola]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DMP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DMP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=VN4:OXIDO(DIOXO)VANADIUM'>VN4</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]] 1.793Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MCP_2127 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=570267 DSM 17711])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=VN4:OXIDO(DIOXO)VANADIUM'>VN4</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5dmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dmp OCA], [~~http~~://pdbe.org/5dmp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5dmp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5dmp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5dmp 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=5dmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dmp OCA], [https://pdbe.org/5dmp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dmp RCSB], [https://www.ebi.ac.uk/pdbsum/5dmp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dmp ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D1Z0H7_METPS D1Z0H7_METPS]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Dsm 17711]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Bartlett, E J~~]]	+	[[Category: Methanocella paludicola]]
-	[[Category: ~~Brissett, N C~~]]	+	[[Category: Bartlett EJ]]
-	[[Category: ~~Doherty, A J~~]]	+	[[Category: Brissett NC]]
-	[[Category: ~~Archaeal protein]]~~	+	[[Category: Doherty AJ]]
-	~~[[Category: Biocatalysis]]~~	+
-	~~[[Category: Dna repair enzyme]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Phosphoric diester hydrolase]]~~	+
-	~~[[Category: Phosphoric monoester hydrolase~~]]	+

OCA at 08:10, 8 April 2020

2020-04-08T08:10:29Z

←Older revision		Revision as of 08:10, 8 April 2020
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	==Structure of the Archaeal NHEJ Phosphoesterase from Methanocella paludicola.==		==Structure of the Archaeal NHEJ Phosphoesterase from Methanocella paludicola.==
-	<StructureSection load='5dmp' size='340' side='right' caption='[[5dmp]], [[Resolution\|resolution]] 1.79Å' scene=''>	+	<StructureSection load='5dmp' size='340' side='right'caption='[[5dmp]], [[Resolution\|resolution]] 1.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dmp]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DMP OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DMP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dmp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dsm_17711 Dsm 17711]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DMP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5DMP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=VN4:OXIDO(DIOXO)VANADIUM'>VN4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=VN4:OXIDO(DIOXO)VANADIUM'>VN4</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=5dmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dmp OCA], [http://pdbe.org/5dmp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dmp RCSB], [http://www.ebi.ac.uk/pdbsum/5dmp PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MCP_2127 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=570267 DSM 17711])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5dmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dmp OCA], [http://pdbe.org/5dmp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dmp RCSB], [http://www.ebi.ac.uk/pdbsum/5dmp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dmp ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Dsm 17711]]
		+	[[Category: Large Structures]]
	[[Category: Bartlett, E J]]		[[Category: Bartlett, E J]]
	[[Category: Brissett, N C]]		[[Category: Brissett, N C]]

OCA at 16:17, 10 May 2016

2016-05-10T16:17:02Z

←Older revision		Revision as of 16:17, 10 May 2016
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		+
	==Structure of the Archaeal NHEJ Phosphoesterase from Methanocella paludicola.==		==Structure of the Archaeal NHEJ Phosphoesterase from Methanocella paludicola.==
	<StructureSection load='5dmp' size='340' side='right' caption='[[5dmp]], [[Resolution\|resolution]] 1.79Å' scene=''>		<StructureSection load='5dmp' size='340' side='right' caption='[[5dmp]], [[Resolution\|resolution]] 1.79Å' scene=''>

OCA at 13:45, 7 October 2015

2015-10-07T13:45:50Z

←Older revision		Revision as of 13:45, 7 October 2015
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-	'''~~Unreleased~~ structure'''	+	==Structure of the Archaeal NHEJ Phosphoesterase from Methanocella paludicola.==
		+	<StructureSection load='5dmp' size='340' side='right' caption='[[5dmp]], [[Resolution\|resolution]] 1.79Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5dmp]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DMP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DMP FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=VN4:OXIDO(DIOXO)VANADIUM'>VN4</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=5dmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dmp OCA], [http://pdbe.org/5dmp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dmp RCSB], [http://www.ebi.ac.uk/pdbsum/5dmp PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The non-homologous end-joining (NHEJ) pathway repairs DNA double-strand breaks (DSBs) in all domains of life. Archaea and bacteria utilize a conserved set of multifunctional proteins in a pathway termed Archaeo-Prokaryotic (AP) NHEJ that facilitates DSB repair. Archaeal NHEJ polymerases (Pol) are capable of strand displacement synthesis, whilst filling DNA gaps or partially annealed DNA ends, which can give rise to unligatable intermediates. However, an associated NHEJ phosphoesterase (PE) resects these products to ensure that efficient ligation occurs. Here, we describe the crystal structures of these archaeal (Methanocella paludicola) NHEJ nuclease and polymerase enzymes, demonstrating their strict structural conservation with their bacterial NHEJ counterparts. Structural analysis, in conjunction with biochemical studies, has uncovered the molecular basis for DNA strand displacement synthesis in AP-NHEJ, revealing the mechanisms that enable Pol and PE to displace annealed bases to facilitate their respective roles in DSB repair.

-	~~The entry 5dmp is ON HOLD until Paper Publication~~	+	Molecular basis for DNA strand displacement by NHEJ repair polymerases.,Bartlett EJ, Brissett NC, Plocinski P, Carlberg T, Doherty AJ Nucleic Acids Res. 2015 Sep 23. pii: gkv965. PMID:26405198<ref>PMID:26405198</ref>

-	~~Authors: Brissett~~, N.C.~~, Bartlett, E.J., Doherty, A.J~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Structure of the Archaeal NHEJ Phosphoesterase from Methanocella paludicola.~~	+	<div class="pdbe-citations 5dmp" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
-	[[Category: Brissett, N.C]]	+	<references/>
-	[[Category: Doherty, A.J]]	+	__TOC__
-	[[Category: ~~Bartlett, E.J~~]]	+	</StructureSection>
		+	[[Category: Bartlett, E J]]
		+	[[Category: Brissett, N C]]
		+	[[Category: Doherty, A J]]
		+	[[Category: Archaeal protein]]
		+	[[Category: Biocatalysis]]
		+	[[Category: Dna repair enzyme]]
		+	[[Category: Hydrolase]]
		+	[[Category: Phosphoric diester hydrolase]]
		+	[[Category: Phosphoric monoester hydrolase]]

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

2015-09-30T13:10:48Z

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

←Older revision

Revision as of 13:10, 30 September 2015

OCA: New page: '''Unreleased structure''' The entry 5dmp is ON HOLD until Paper Publication Authors: Brissett, N.C., Bartlett, E.J., Doherty, A.J. Description: Structure of the Archaeal NHEJ Phosphoe...

2015-09-30T13:10:46Z

New page: '''Unreleased structure''' The entry 5dmp is ON HOLD until Paper Publication Authors: Brissett, N.C., Bartlett, E.J., Doherty, A.J. Description: Structure of the Archaeal NHEJ Phosphoe...

New page

'''Unreleased structure'''

The entry 5dmp is ON HOLD until Paper Publication

Authors: Brissett, N.C., Bartlett, E.J., Doherty, A.J.

Description: Structure of the Archaeal NHEJ Phosphoesterase from Methanocella paludicola.
[[Category: Unreleased Structures]]
[[Category: Brissett, N.C]]
[[Category: Doherty, A.J]]
[[Category: Bartlett, E.J]]