5txx - Revision history

OCA at 13:15, 4 October 2023

OCA — Wed, 04 Oct 2023 13:15:47 GMT

←Older revision		Revision as of 13:15, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='5txx' size='340' side='right'caption='[[5txx]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='5txx' size='340' side='right'caption='[[5txx]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5txx]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TXX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TXX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5txx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TXX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TXX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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]] 1.948Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5txz\|5txz]], [[5tyb\|5tyb]], [[5tyc\|5tyc]], [[5tyd\|5tyd]], [[5tye\|5tye]], [[5tyf\|5tyf]], [[5tyg\|5tyg]], [[5tyu\|5tyu]], [[5tyv\|5tyv]], [[5tyw\|5tyw]], [[5tyx\|5tyx]], [[5tyy\|5tyy]], [[5tyz\|5tyz]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLM, polmu ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5txx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5txx OCA], [https://pdbe.org/5txx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5txx RCSB], [https://www.ebi.ac.uk/pdbsum/5txx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5txx ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=5txx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5txx OCA], [~~http~~://pdbe.org/5txx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5txx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5txx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5txx ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DPOLM_HUMAN DPOLM_HUMAN]] Gap-filling polymerase involved in repair of DNA double-strand breaks by non-homologous end joining (NHEJ). Participates in immunoglobulin (Ig) light chain gene rearrangement in V(D)J recombination.<ref>PMID:12640116</ref> <ref>PMID:12888504</ref> <ref>PMID:17483519</ref> <ref>PMID:17915942</ref>	+	[https://www.uniprot.org/uniprot/DPOLM_HUMAN DPOLM_HUMAN] Gap-filling polymerase involved in repair of DNA double-strand breaks by non-homologous end joining (NHEJ). Participates in immunoglobulin (Ig) light chain gene rearrangement in V(D)J recombination.<ref>PMID:12640116</ref> <ref>PMID:12888504</ref> <ref>PMID:17483519</ref> <ref>PMID:17915942</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 22:
	==See Also==		==See Also==
	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]		*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
-	*[[RNA polymerase\|RNA polymerase]]	+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~DNA-directed DNA polymerase]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Jamsen, J A~~]]	+	[[Category: Unidentified]]
-	[[Category: ~~Wilson, S H~~]]	+	[[Category: Jamsen JA]]
-	[[Category: ~~Dna polymerase mu]]~~	+	[[Category: Wilson SH]]
-	~~[[Category: Double strand break repair]]~~	+
-	~~[[Category: Product metal]]~~	+
-	~~[[Category: Time-lapse crystallography]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 09:03, 18 December 2019

OCA — Wed, 18 Dec 2019 09:03:22 GMT

←Older revision		Revision as of 09:03, 18 December 2019
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	==DNA Polymerase Mu Pre-Catalytic Ground State Ternary Complex, Ca2+==		==DNA Polymerase Mu Pre-Catalytic Ground State Ternary Complex, Ca2+==
-	<StructureSection load='5txx' size='340' side='right' caption='[[5txx]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='5txx' size='340' side='right'caption='[[5txx]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5txx]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TXX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TXX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5txx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TXX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TXX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5txz\|5txz]], [[5tyb\|5tyb]], [[5tyc\|5tyc]], [[5tyd\|5tyd]], [[5tye\|5tye]], [[5tyf\|5tyf]], [[5tyg\|5tyg]], [[5tyu\|5tyu]], [[5tyv\|5tyv]], [[5tyw\|5tyw]], [[5tyx\|5tyx]], [[5tyy\|5tyy]], [[5tyz\|5tyz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5txz\|5txz]], [[5tyb\|5tyb]], [[5tyc\|5tyc]], [[5tyd\|5tyd]], [[5tye\|5tye]], [[5tyf\|5tyf]], [[5tyg\|5tyg]], [[5tyu\|5tyu]], [[5tyv\|5tyv]], [[5tyw\|5tyw]], [[5tyx\|5tyx]], [[5tyy\|5tyy]], [[5tyz\|5tyz]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLM, polmu ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=5txx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5txx OCA], [http://pdbe.org/5txx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5txx RCSB], [http://www.ebi.ac.uk/pdbsum/5txx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5txx 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=5txx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5txx OCA], [http://pdbe.org/5txx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5txx RCSB], [http://www.ebi.ac.uk/pdbsum/5txx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5txx ProSAT]</span></td></tr>
Line 20:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5txx" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5txx" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
		+	*[[RNA polymerase\|RNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Jamsen, J A]]		[[Category: Jamsen, J A]]
	[[Category: Wilson, S H]]		[[Category: Wilson, S H]]

OCA at 03:54, 30 August 2017

OCA — Wed, 30 Aug 2017 03:54:55 GMT

←Older revision		Revision as of 03:54, 30 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5txx is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==DNA Polymerase Mu Pre-Catalytic Ground State Ternary Complex, Ca2+==
		+	<StructureSection load='5txx' size='340' side='right' caption='[[5txx]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5txx]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TXX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TXX FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5txz\|5txz]], [[5tyb\|5tyb]], [[5tyc\|5tyc]], [[5tyd\|5tyd]], [[5tye\|5tye]], [[5tyf\|5tyf]], [[5tyg\|5tyg]], [[5tyu\|5tyu]], [[5tyv\|5tyv]], [[5tyw\|5tyw]], [[5tyx\|5tyx]], [[5tyy\|5tyy]], [[5tyz\|5tyz]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=5txx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5txx OCA], [http://pdbe.org/5txx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5txx RCSB], [http://www.ebi.ac.uk/pdbsum/5txx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5txx ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPOLM_HUMAN DPOLM_HUMAN]] Gap-filling polymerase involved in repair of DNA double-strand breaks by non-homologous end joining (NHEJ). Participates in immunoglobulin (Ig) light chain gene rearrangement in V(D)J recombination.<ref>PMID:12640116</ref> <ref>PMID:12888504</ref> <ref>PMID:17483519</ref> <ref>PMID:17915942</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA polymerase (pol) mu is a DNA-dependent polymerase that incorporates nucleotides during gap-filling synthesis in the non-homologous end-joining pathway of double-strand break repair. Here we report time-lapse X-ray crystallography snapshots of catalytic events during gap-filling DNA synthesis by pol mu. Unique catalytic intermediates and active site conformational changes that underlie catalysis are uncovered, and a transient third (product) metal ion is observed in the product state. The product manganese coordinates phosphate oxygens of the inserted nucleotide and PPi. The product metal is not observed during DNA synthesis in the presence of magnesium. Kinetic analyses indicate that manganese increases the rate constant for deoxynucleoside 5'-triphosphate insertion compared to magnesium. The likely product stabilization role of the manganese product metal in pol mu is discussed. These observations provide insight on structural attributes of this X-family double-strand break repair polymerase that impact its biological function in genome maintenance.DNA polymerase (pol) mu functions in DNA double-strand break repair. Here the authors use time-lapse X-ray crystallography to capture the states of pol micro during the conversion from pre-catalytic to product complex and observe a third transiently bound metal ion in the product state.

-	~~Authors~~:	+	Time-lapse crystallography snapshots of a double-strand break repair polymerase in action.,Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF, Krahn JM, Bebenek K, Kunkel TA, Wilson SH Nat Commun. 2017 Aug 15;8(1):253. doi: 10.1038/s41467-017-00271-7. PMID:28811466<ref>PMID:28811466</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5txx" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Jamsen, J A]]
		+	[[Category: Wilson, S H]]
		+	[[Category: Dna polymerase mu]]
		+	[[Category: Double strand break repair]]
		+	[[Category: Product metal]]
		+	[[Category: Time-lapse crystallography]]
		+	[[Category: Transferase-dna complex]]

OCA at 10:47, 5 April 2017

OCA — Wed, 05 Apr 2017 10:47:17 GMT

←Older revision		Revision as of 10:47, 5 April 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Fri, 09 Dec 2016 18:02:28 GMT

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

←Older revision

Revision as of 18:02, 9 December 2016

OCA: New page: '''Unreleased structure''' The entry 5txx is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Fri, 09 Dec 2016 18:02:27 GMT

New page: '''Unreleased structure''' The entry 5txx is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5txx is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]