5vzh - Revision history

OCA at 14:03, 4 October 2023

OCA — Wed, 04 Oct 2023 14:03:30 GMT

←Older revision		Revision as of 14:03, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='5vzh' size='340' side='right'caption='[[5vzh]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='5vzh' size='340' side='right'caption='[[5vzh]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vzh]] 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=5VZH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VZH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vzh]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VZH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VZH 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOA:GLYCOLIC+ACID'>GOA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</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]] 1.95Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5twp\|5twp]], [[5twq\|5twq]], [[5twr\|5twr]], [[5tws\|5tws]]</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOA:GLYCOLIC+ACID'>GOA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</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=5vzh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vzh OCA], [https://pdbe.org/5vzh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vzh RCSB], [https://www.ebi.ac.uk/pdbsum/5vzh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vzh 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=5vzh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vzh OCA], [~~http~~://pdbe.org/5vzh PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vzh RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vzh PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vzh 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 ==
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	==See Also==		==See Also==
-	*[[RNA polymerase\|RNA polymerase]]	+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
		+	*[[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: Bebenek, K]]	+	[[Category: Synthetic construct]]
-	[[Category: Kunkel~~, T A~~]]	+	[[Category: Bebenek K]]
-	[[Category: Moon~~, A F~~]]	+	[[Category: Kunkel TA]]
-	[[Category: Pedersen~~, L C~~]]	+	[[Category: Moon AF]]
-	[[Category: Pryor~~, J M~~]]	+	[[Category: Pedersen LC]]
-	[[Category: Ramsden~~, D A]]~~	+	[[Category: Pryor JM]]
-	~~[[Category: Dna double strand break repair]]~~	+	[[Category: Ramsden DA]]
-	~~[[Category: Family x dna polymerase]]~~	+
-	~~[[Category: Nonhomologous end-joining]]~~	+
-	~~[[Category: Ribonucleotide incorporation]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 09:39, 4 December 2019

OCA — Wed, 04 Dec 2019 09:39:17 GMT

←Older revision		Revision as of 09:39, 4 December 2019
Line 1:		Line 1:

	==Post-catalytic complex of human Polymerase Mu (W434H) mutant with incoming UTP==		==Post-catalytic complex of human Polymerase Mu (W434H) mutant with incoming UTP==
-	<StructureSection load='5vzh' size='340' side='right' caption='[[5vzh]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='5vzh' size='340' side='right'caption='[[5vzh]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vzh]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VZH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VZH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vzh]] 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=5VZH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VZH 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOA:GLYCOLIC+ACID'>GOA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</scene></td></tr>		</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOA:GLYCOLIC+ACID'>GOA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5twp\|5twp]], [[5twq\|5twq]], [[5twr\|5twr]], [[5tws\|5tws]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5twp\|5twp]], [[5twq\|5twq]], [[5twr\|5twr]], [[5tws\|5tws]]</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=5vzh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vzh OCA], [http://pdbe.org/5vzh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vzh RCSB], [http://www.ebi.ac.uk/pdbsum/5vzh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vzh 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=5vzh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vzh OCA], [http://pdbe.org/5vzh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vzh RCSB], [http://www.ebi.ac.uk/pdbsum/5vzh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vzh ProSAT]</span></td></tr>
Line 20:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5vzh" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5vzh" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[RNA polymerase\|RNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Bebenek, K]]		[[Category: Bebenek, K]]
	[[Category: Kunkel, T A]]		[[Category: Kunkel, T A]]

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

OCA — Wed, 27 Sep 2017 10:02:42 GMT

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

←Older revision

Revision as of 10:02, 27 September 2017

OCA: New page: ==Post-catalytic complex of human Polymerase Mu (W434H) mutant with incoming UTP== == Structural highlights ==
<table><tr><td colspan='2'>[[5vzh]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VZH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VZH 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOA:GLYCOLIC+ACID'>GOA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5twp|5twp]], [[5twq|5twq]], [[5twr|5twr]], [[5tws|5tws]]</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=5vzh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vzh OCA], [http://pdbe.org/5vzh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vzh RCSB], [http://www.ebi.ac.uk/pdbsum/5vzh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vzh 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 ==
While most DNA polymerases discriminate against ribonucleotide triphosphate (rNTP) incorporation very effectively, the Family X member DNA polymerase mu (Pol mu) incorporates rNTPs almost as efficiently as deoxyribonucleotides. To gain insight into how this occurs, here we have used X-ray crystallography to describe the structures of pre- and post-catalytic complexes of Pol mu with a ribonucleotide bound at the active site. These structures reveal that Pol mu binds and incorporates a rNTP with normal active site geometry and no distortion of the DNA substrate or nucleotide. Moreover, a comparison of rNTP incorporation kinetics by wildtype and mutant Pol mu indicates that rNTP accommodation involves synergistic interactions with multiple active site residues not found in polymerases with greater discrimination. Together, the results are consistent with the hypothesis that rNTP incorporation by Pol mu is advantageous in gap-filling synthesis during DNA double strand break repair by nonhomologous end joining, particularly in nonreplicating cells containing very low deoxyribonucleotide concentrations.

Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu.,Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC Nucleic Acids Res. 2017 Sep 6;45(15):9138-9148. doi: 10.1093/nar/gkx527. PMID:28911097<ref>PMID:28911097</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5vzh" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[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 double strand break repair]]
[[Category: Family x dna polymerase]]
[[Category: Nonhomologous end-joining]]
[[Category: Ribonucleotide incorporation]]
[[Category: Transferase-dna complex]]