5txz - Revision history

OCA at 15:43, 6 March 2024

2024-03-06T15:43:52Z

←Older revision		Revision as of 15:43, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='5txz' size='340' side='right'caption='[[5txz]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='5txz' size='340' side='right'caption='[[5txz]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5txz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TXZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5TXZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5txz]] 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=5TXZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TXZ FirstGlance]. <br>
-	</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=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</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]] 1.651Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5txx\|5txx]], [[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=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=5txz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5txz OCA], [https://pdbe.org/5txz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5txz RCSB], [https://www.ebi.ac.uk/pdbsum/5txz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5txz ProSAT]</span></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=5txz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5txz OCA], [~~http~~://pdbe.org/5txz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5txz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5txz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5txz 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;">~~	+
-	~~== 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.	+
-		+
-	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>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5txz" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 28:		Line 18:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~DNA-directed DNA polymerase~~]]	+	[[Category: Homo sapiens]]
	[[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 12:22, 23 September 2020

2020-09-23T12:22:43Z

←Older revision		Revision as of 12:22, 23 September 2020
Line 1:		Line 1:

	==DNA Polymerase Mu Reactant Complex, 100mM Mg2+ (15 min)==		==DNA Polymerase Mu Reactant Complex, 100mM Mg2+ (15 min)==
-	<StructureSection load='5txz' size='340' side='right' caption='[[5txz]], [[Resolution\|resolution]] 1.65Å' scene=''>	+	<StructureSection load='5txz' size='340' side='right'caption='[[5txz]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5txz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TXZ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TXZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5txz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TXZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5TXZ 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=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</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" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</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">[[5txx\|5txx]], [[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">[[5txx\|5txx]], [[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='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=5txz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5txz OCA], [http://pdbe.org/5txz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5txz RCSB], [http://www.ebi.ac.uk/pdbsum/5txz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5txz ProSAT]</span></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=5txz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5txz OCA], [http://pdbe.org/5txz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5txz RCSB], [http://www.ebi.ac.uk/pdbsum/5txz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5txz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5txz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5txz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
		+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Jamsen, J A]]		[[Category: Jamsen, J A]]
	[[Category: Wilson, S H]]		[[Category: Wilson, S H]]

OCA at 04:07, 30 August 2017

2017-08-30T04:07:31Z

←Older revision		Revision as of 04:07, 30 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5txz is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==DNA Polymerase Mu Reactant Complex, 100mM Mg2+ (15 min)==
		+	<StructureSection load='5txz' size='340' side='right' caption='[[5txz]], [[Resolution\|resolution]] 1.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5txz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TXZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TXZ 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=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</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">[[5txx\|5txx]], [[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=5txz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5txz OCA], [http://pdbe.org/5txz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5txz RCSB], [http://www.ebi.ac.uk/pdbsum/5txz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5txz 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 5txz" 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

2017-04-05T10:47:22Z

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

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

	Authors:		Authors:

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

2016-12-09T18:02:37Z

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

←Older revision

Revision as of 18:02, 9 December 2016

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

2016-12-09T18:02:36Z

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

New page

'''Unreleased structure'''

The entry 5txz is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]