5dmu - Revision history

OCA at 21:50, 28 June 2023

OCA — Wed, 28 Jun 2023 21:50:22 GMT

←Older revision		Revision as of 21:50, 28 June 2023
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	<StructureSection load='5dmu' size='340' side='right'caption='[[5dmu]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='5dmu' size='340' side='right'caption='[[5dmu]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dmu]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Metps Metps~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DMU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5DMU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dmu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocella_paludicola_SANAE Methanocella paludicola SANAE]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DMU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DMU 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.949Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MCP_2125 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=304371 METPS])~~</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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~~://proteopedia.org/fgij/fg.htm?mol=5dmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dmu OCA], [~~http~~://pdbe.org/5dmu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5dmu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5dmu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5dmu 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=5dmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dmu OCA], [https://pdbe.org/5dmu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dmu RCSB], [https://www.ebi.ac.uk/pdbsum/5dmu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dmu ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D1Z0H5_METPS D1Z0H5_METPS]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Metps~~]]	+	[[Category: Methanocella paludicola SANAE]]
-	[[Category: Bartlett~~, E J~~]]	+	[[Category: Bartlett EJ]]
-	[[Category: Brissett~~, N C~~]]	+	[[Category: Brissett NC]]
-	[[Category: Doherty~~, A J]]~~	+	[[Category: Doherty AJ]]
-	~~[[Category: Archaeal protein]]~~	+
-	~~[[Category: Biocatalysis]]~~	+
-	~~[[Category: Dna repair enzyme]]~~	+
-	~~[[Category: Dna-directed dna polymerase]]~~	+
-	~~[[Category: Protein structure]]~~	+
-	~~[[Category: Ribonucleotide]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:10, 8 April 2020

OCA — Wed, 08 Apr 2020 08:10:45 GMT

←Older revision		Revision as of 08:10, 8 April 2020
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	==Structure of the NHEJ polymerase from Methanocella paludicola==		==Structure of the NHEJ polymerase from Methanocella paludicola==
-	<StructureSection load='5dmu' size='340' side='right' caption='[[5dmu]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='5dmu' size='340' side='right'caption='[[5dmu]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dmu]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DMU OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DMU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dmu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Metps Metps]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DMU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5DMU 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=5dmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dmu OCA], [http://pdbe.org/5dmu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dmu RCSB], [http://www.ebi.ac.uk/pdbsum/5dmu PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MCP_2125 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=304371 METPS])</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=5dmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dmu OCA], [http://pdbe.org/5dmu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dmu RCSB], [http://www.ebi.ac.uk/pdbsum/5dmu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dmu 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: Large Structures]]
		+	[[Category: Metps]]
	[[Category: Bartlett, E J]]		[[Category: Bartlett, E J]]
	[[Category: Brissett, N C]]		[[Category: Brissett, N C]]

OCA at 16:48, 10 May 2016

OCA — Tue, 10 May 2016 16:48:47 GMT

←Older revision		Revision as of 16:48, 10 May 2016
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		+
	==Structure of the NHEJ polymerase from Methanocella paludicola==		==Structure of the NHEJ polymerase from Methanocella paludicola==
	<StructureSection load='5dmu' size='340' side='right' caption='[[5dmu]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='5dmu' size='340' side='right' caption='[[5dmu]], [[Resolution\|resolution]] 1.95Å' scene=''>

OCA at 13:41, 7 October 2015

OCA — Wed, 07 Oct 2015 13:41:01 GMT

←Older revision		Revision as of 13:41, 7 October 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Structure of the NHEJ polymerase from Methanocella paludicola==
		+	<StructureSection load='5dmu' size='340' side='right' caption='[[5dmu]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5dmu]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DMU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DMU 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=5dmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dmu OCA], [http://pdbe.org/5dmu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dmu RCSB], [http://www.ebi.ac.uk/pdbsum/5dmu 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 5dmu 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 NHEJ polymerase from Methanocella paludicola~~	+	<div class="pdbe-citations 5dmu" 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: Dna-directed dna polymerase]]
		+	[[Category: Protein structure]]
		+	[[Category: Ribonucleotide]]
		+	[[Category: Transferase]]

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

OCA — Wed, 30 Sep 2015 13:11:11 GMT

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

←Older revision

Revision as of 13:11, 30 September 2015

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

OCA — Wed, 30 Sep 2015 13:11:10 GMT

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

New page

'''Unreleased structure'''

The entry 5dmu is ON HOLD until Paper Publication

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

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