5vzd - Revision history

OCA at 14:03, 4 October 2023

OCA — Wed, 04 Oct 2023 14:03:22 GMT

←Older revision		Revision as of 14:03, 4 October 2023
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	<StructureSection load='5vzd' size='340' side='right'caption='[[5vzd]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='5vzd' size='340' side='right'caption='[[5vzd]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vzd]] 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=5VZD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VZD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vzd]] 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=5VZD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VZD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2KH:5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]URIDINE'>2KH</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]] 1.602Å</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=2KH:5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]URIDINE'>2KH</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='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=5vzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vzd OCA], [https://pdbe.org/5vzd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vzd RCSB], [https://www.ebi.ac.uk/pdbsum/5vzd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vzd 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=5vzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vzd OCA], [~~http~~://pdbe.org/5vzd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vzd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vzd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vzd 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 23:		Line 21:

	==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 09:38, 4 December 2019

OCA — Wed, 04 Dec 2019 09:38:51 GMT

←Older revision		Revision as of 09:38, 4 December 2019
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	==Pre-catalytic ternary complex of human Polymerase Mu (W434A) mutant with incoming nonhydrolyzable UMPNPP==		==Pre-catalytic ternary complex of human Polymerase Mu (W434A) mutant with incoming nonhydrolyzable UMPNPP==
-	<StructureSection load='5vzd' size='340' side='right' caption='[[5vzd]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='5vzd' size='340' side='right'caption='[[5vzd]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vzd]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VZD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VZD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vzd]] 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=5VZD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VZD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2KH:5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]URIDINE'>2KH</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"><scene name='pdbligand=2KH:5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]URIDINE'>2KH</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">[[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=5vzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vzd OCA], [http://pdbe.org/5vzd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vzd RCSB], [http://www.ebi.ac.uk/pdbsum/5vzd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vzd 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=5vzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vzd OCA], [http://pdbe.org/5vzd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vzd RCSB], [http://www.ebi.ac.uk/pdbsum/5vzd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vzd ProSAT]</span></td></tr>
Line 20:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5vzd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5vzd" 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 "5vzd" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 09:49:58 GMT

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

←Older revision

Revision as of 09:49, 27 September 2017

OCA: New page: ==Pre-catalytic ternary complex of human Polymerase Mu (W434A) mutant with incoming nonhydrolyzable UMPNPP== == Structural highlights ==
<table><tr><td colspan='2'>[[5vzd]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VZD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VZD FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2KH:5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]URIDINE'>2KH</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">[[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=5vzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vzd OCA], [http://pdbe.org/5vzd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vzd RCSB], [http://www.ebi.ac.uk/pdbsum/5vzd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vzd 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 5vzd" 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]]