4m04 - Revision history

OCA at 16:29, 20 September 2023

2023-09-20T16:29:49Z

←Older revision		Revision as of 16:29, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4m04]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M04 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4M04 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4m04]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M04 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4M04 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</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></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]] 1.898Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</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></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=4m04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m04 OCA], [https://pdbe.org/4m04 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4m04 RCSB], [https://www.ebi.ac.uk/pdbsum/4m04 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4m04 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=4m04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m04 OCA], [https://pdbe.org/4m04 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4m04 RCSB], [https://www.ebi.ac.uk/pdbsum/4m04 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4m04 ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:

	==See Also==		==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]		*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	== References ==		== References ==

OCA at 10:44, 21 December 2022

2022-12-21T10:44:45Z

←Older revision		Revision as of 10:44, 21 December 2022
Line 1:		Line 1:

	==Human DNA Polymerase Mu ternary complex==		==Human DNA Polymerase Mu ternary complex==
-	<StructureSection load='4m04' size='340' side='right' caption='[[4m04]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='4m04' size='340' side='right'caption='[[4m04]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4m04]] 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=4M04 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4M04 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4m04]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M04 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4M04 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</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~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</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></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ihm\|2ihm]], [[4lzd\|4lzd]], [[4lzg\|4lzg]], [[4m0a\|4m0a]]</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=4m04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m04 OCA], [https://pdbe.org/4m04 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4m04 RCSB], [https://www.ebi.ac.uk/pdbsum/4m04 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4m04 ProSAT]</span></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='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=4m04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m04 OCA], [~~http~~://pdbe.org/4m04 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4m04 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4m04 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4m04 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 21:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4m04" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4m04" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[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: Bebenek, K]]	+	[[Category: Bebenek K]]
-	[[Category: Kunkel~~, T A~~]]	+	[[Category: Kunkel TA]]
-	[[Category: Moon~~, A F~~]]	+	[[Category: Moon AF]]
-	[[Category: Pedersen~~, L C~~]]	+	[[Category: Pedersen LC]]
-	[[Category: Pryor~~, J M~~]]	+	[[Category: Pryor JM]]
-	[[Category: Ramsden~~, D A]]~~	+	[[Category: Ramsden DA]]
-	~~[[Category: Dna break repair]]~~	+
-	~~[[Category: Polymerase]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 09:45, 15 November 2017

2017-11-15T09:45:30Z

←Older revision		Revision as of 09:45, 15 November 2017
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	</div>		</div>
	<div class="pdbe-citations 4m04" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4m04" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[RNA polymerase\|RNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:12, 4 August 2016

2016-08-04T08:12:20Z

←Older revision		Revision as of 08:12, 4 August 2016
Line 1:		Line 1:
		+
	==Human DNA Polymerase Mu ternary complex==		==Human DNA Polymerase Mu ternary complex==
	<StructureSection load='4m04' size='340' side='right' caption='[[4m04]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4m04' size='340' side='right' caption='[[4m04]], [[Resolution\|resolution]] 1.90Å' scene=''>
Line 7:		Line 8:
	<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='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=4m04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m04 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4m04 RCSB], [http://www.ebi.ac.uk/pdbsum/4m04 PDBsum]</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=4m04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m04 OCA], [http://pdbe.org/4m04 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4m04 RCSB], [http://www.ebi.ac.uk/pdbsum/4m04 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4m04 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4m04" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 07:29, 24 December 2014

2014-12-24T07:29:36Z

←Older revision		Revision as of 07:29, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4m04]] 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=4M04 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4M04 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4m04]] 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=4M04 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4M04 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</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><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</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></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ihm\|2ihm]], [[4lzd\|4lzd]], [[4lzg\|4lzg]], [[4m0a\|4m0a]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ihm\|2ihm]], [[4lzd\|4lzd]], [[4lzg\|4lzg]], [[4m0a\|4m0a]]</td></tr>
-	<tr><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='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><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4m04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m04 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4m04 RCSB], [http://www.ebi.ac.uk/pdbsum/4m04 PDBsum]</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=4m04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m04 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4m04 RCSB], [http://www.ebi.ac.uk/pdbsum/4m04 PDBsum]</span></td></tr>
-	<table>	+	</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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 17:
	Sustained active site rigidity during synthesis by human DNA polymerase mu.,Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC Nat Struct Mol Biol. 2014 Mar;21(3):253-60. doi: 10.1038/nsmb.2766. Epub 2014 Feb, 2. PMID:24487959<ref>PMID:24487959</ref>		Sustained active site rigidity during synthesis by human DNA polymerase mu.,Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC Nat Struct Mol Biol. 2014 Mar;21(3):253-60. doi: 10.1038/nsmb.2766. Epub 2014 Feb, 2. PMID:24487959<ref>PMID:24487959</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+
		+	==See Also==
		+	*[[RNA polymerase\|RNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>
Line 23:		Line 28:
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Human]]		[[Category: Human]]
-	[[Category: Bebenek, K.]]	+	[[Category: Bebenek, K]]
-	[[Category: Kunkel, T A.]]	+	[[Category: Kunkel, T A]]
-	[[Category: Moon, A F.]]	+	[[Category: Moon, A F]]
-	[[Category: Pedersen, L C.]]	+	[[Category: Pedersen, L C]]
-	[[Category: Pryor, J M.]]	+	[[Category: Pryor, J M]]
-	[[Category: Ramsden, D A.]]	+	[[Category: Ramsden, D A]]
	[[Category: Dna break repair]]		[[Category: Dna break repair]]
	[[Category: Polymerase]]		[[Category: Polymerase]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 13:33, 18 May 2014

2014-05-18T13:33:37Z

←Older revision		Revision as of 13:33, 18 May 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4m04\| PDB~~=4m04 \| ~~SCENE~~= }}	+	==Human DNA Polymerase Mu ternary complex==
-	===Human DNA ~~Polymerase Mu ternary complex~~===	+	<StructureSection load='4m04' size='340' side='right' caption='[[4m04]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24487959}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4m04]] 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=4M04 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4M04 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</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><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ihm\|2ihm]], [[4lzd\|4lzd]], [[4lzg\|4lzg]], [[4m0a\|4m0a]]</td></tr>
		+	<tr><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><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4m04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m04 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4m04 RCSB], [http://www.ebi.ac.uk/pdbsum/4m04 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA polymerase mu (Pol mu) is the only template-dependent human DNA polymerase capable of repairing double-strand DNA breaks (DSBs) with unpaired 3' ends in nonhomologous end joining (NHEJ). To probe this function, we structurally characterized Pol mu's catalytic cycle for single-nucleotide incorporation. These structures indicate that, unlike other template-dependent DNA polymerases, Pol mu shows no large-scale conformational changes in protein subdomains, amino acid side chains or DNA upon dNTP binding or catalysis. Instead, the only major conformational change is seen earlier in the catalytic cycle, when the flexible loop 1 region repositions upon DNA binding. Pol mu variants with changes in loop 1 have altered catalytic properties and are partially defective in NHEJ. The results indicate that specific loop 1 residues contribute to Pol mu's unique ability to catalyze template-dependent NHEJ of DSBs with unpaired 3' ends.

-	~~==Function==~~	+	Sustained active site rigidity during synthesis by human DNA polymerase mu.,Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC Nat Struct Mol Biol. 2014 Mar;21(3):253-60. doi: 10.1038/nsmb.2766. Epub 2014 Feb, 2. PMID:24487959<ref>PMID:24487959</ref>
-	~~[[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>	+

-	~~==About this Structure==~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4m04]] is~~ a ~~4 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4M04 OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:024487959</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Human]]
	[[Category: Bebenek, K.]]		[[Category: Bebenek, K.]]
	[[Category: Kunkel, T A.]]		[[Category: Kunkel, T A.]]

OCA at 08:48, 19 March 2014

2014-03-19T08:48:28Z

←Older revision		Revision as of 08:48, 19 March 2014
Line 1:		Line 1:
	{{STRUCTURE_4m04\| PDB=4m04 \| SCENE= }}		{{STRUCTURE_4m04\| PDB=4m04 \| SCENE= }}
	===Human DNA Polymerase Mu ternary complex===		===Human DNA Polymerase Mu ternary complex===
		+	{{ABSTRACT_PUBMED_24487959}}

	==Function==		==Function==
Line 9:		Line 10:

	==Reference==		==Reference==
-	<references group="xtra"/><references/>	+	<ref group="xtra">PMID:024487959</ref><references group="xtra"/><references/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Bebenek, K.]]		[[Category: Bebenek, K.]]

OCA at 11:35, 5 February 2014

2014-02-05T11:35:02Z

←Older revision		Revision as of 11:35, 5 February 2014
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4m04\| PDB=4m04 \| SCENE= }}
		+	===Human DNA Polymerase Mu ternary complex===

-	~~The entry 4m04 is ON HOLD~~ ~~until Paper Publication~~	+	==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>

-	~~Authors~~: ~~Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A~~.~~, Bebenek, K~~.~~, Pedersen, L~~.C.	+	==About this Structure==
		+	[[4m04]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M04 OCA].

-	~~Description~~: ~~Human~~ DNA Polymerase ~~Mu ternary~~ complex	+	==Reference==
		+	<references group="xtra"/><references/>
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Bebenek, K.]]
		+	[[Category: Kunkel, T A.]]
		+	[[Category: Moon, A F.]]
		+	[[Category: Pedersen, L C.]]
		+	[[Category: Pryor, J M.]]
		+	[[Category: Ramsden, D A.]]
		+	[[Category: Dna break repair]]
		+	[[Category: Polymerase]]
		+	[[Category: Transferase-dna complex]]

OCA at 07:32, 29 September 2013

2013-09-29T07:32:28Z

←Older revision		Revision as of 07:32, 29 September 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4m04 is ON HOLD	+	The entry 4m04 is ON HOLD until Paper Publication

	Authors: Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.		Authors: Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

	Description: Human DNA Polymerase Mu ternary complex		Description: Human DNA Polymerase Mu ternary complex

OCA at 09:55, 4 September 2013

2013-09-04T09:55:22Z

←Older revision		Revision as of 09:55, 4 September 2013
Line 5:		Line 5:
	Authors: Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.		Authors: Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

-	Description: ternary complex	+	Description: Human DNA Polymerase Mu ternary complex