6ipf - Revision history

OCA at 10:34, 27 March 2024

2024-03-27T10:34:37Z

←Older revision		Revision as of 10:34, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='6ipf' size='340' side='right'caption='[[6ipf]], [[Resolution\|resolution]] 1.77Å' scene=''>		<StructureSection load='6ipf' size='340' side='right'caption='[[6ipf]], [[Resolution\|resolution]] 1.77Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ipf]] 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=6IPF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6IPF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ipf]] 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=6IPF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IPF 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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</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]] 1.77Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</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=6ipf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ipf OCA], [https://pdbe.org/6ipf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ipf RCSB], [https://www.ebi.ac.uk/pdbsum/6ipf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ipf 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=6ipf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ipf OCA], [~~http~~://pdbe.org/6ipf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ipf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ipf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ipf 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 ==~~	+
-	Recent research on the structure and mechanism of DNA polymerases has continued to generate fundamentally important features, including a noncanonical pathway involving "prebinding" of metal-bound dNTP (MdNTP) in the absence of DNA. While this noncanonical mechanism was shown to be a possible subset for African swine fever DNA polymerase X (Pol X) and human Pol lambda, it remains unknown whether it could be the primary pathway for a DNA polymerase. Pol mu is a unique member of the X-family with multiple functions and with unusual Mn(2+) preference. Here we report that Pol mu not only prebinds MdNTP in a catalytically active conformation but also exerts a Mn(2+) over Mg(2+) preference at this early stage of catalysis, for various functions: incorporation of dNTP into a single nucleotide gapped DNA, incorporation of rNTP in the nonhomologous end joining (NHEJ) repair, incorporation of dNTP to an ssDNA, and incorporation of an 8-oxo-dGTP opposite template dA (mismatched) or dC (matched). The structural basis of this noncanonical mechanism and Mn(2+) over Mg(2+) preference in these functions was analyzed by solving 19 structures of prebinding binary complexes, precatalytic ternary complexes, and product complexes. The results suggest that the noncanonical pathway is functionally relevant for the multiple functions of Pol mu. Overall, this work provides the structural and mechanistic basis for the long-standing puzzle in the Mn(2+) preference of Pol mu and expands the landscape of the possible mechanisms of DNA polymerases to include both mechanistic pathways.	+

-	Human DNA Polymerase mu Can Use a Noncanonical Mechanism for Multiple Mn(2+)-Mediated Functions.,Chang YK, Huang YP, Liu XX, Ko TP, Bessho Y, Kawano Y, Maestre-Reyna M, Wu WJ, Tsai MD J Am Chem Soc. 2019 May 17. doi: 10.1021/jacs.9b01741. PMID:31067051<ref>PMID:31067051</ref>	+	==See Also==
-		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 6ipf" style~~=~~"background-color:#fffaf0;"></div>~~	+
	== 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: ~~Chang, Y K~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Tsai, M D~~]]	+	[[Category: Chang YK]]
-	[[Category: ~~Wu, W J~~]]	+	[[Category: Tsai MD]]
-	[[Category: ~~8-oxo-dgtp]]~~	+	[[Category: Wu WJ]]
-	~~[[Category: Dna break repair]]~~	+
-	~~[[Category: Dna polymerase mu]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 06:14, 12 June 2019

2019-06-12T06:14:22Z

←Older revision		Revision as of 06:14, 12 June 2019
Line 3:		Line 3:
	<StructureSection load='6ipf' size='340' side='right'caption='[[6ipf]], [[Resolution\|resolution]] 1.77Å' scene=''>		<StructureSection load='6ipf' size='340' side='right'caption='[[6ipf]], [[Resolution\|resolution]] 1.77Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ipf]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IPF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IPF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ipf]] 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=6IPF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IPF 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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</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='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=6ipf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ipf OCA], [http://pdbe.org/6ipf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ipf RCSB], [http://www.ebi.ac.uk/pdbsum/6ipf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ipf 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=6ipf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ipf OCA], [http://pdbe.org/6ipf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ipf RCSB], [http://www.ebi.ac.uk/pdbsum/6ipf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ipf ProSAT]</span></td></tr>
Line 25:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Chang, Y K]]		[[Category: Chang, Y K]]

OCA at 06:10, 29 May 2019

2019-05-29T06:10:41Z

←Older revision		Revision as of 06:10, 29 May 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ipf is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Post-catalytic Complex of Human DNA Polymerase Mu with Templating Cytosine and Mn-8oxodGMP==
		+	<StructureSection load='6ipf' size='340' side='right'caption='[[6ipf]], [[Resolution\|resolution]] 1.77Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6ipf]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IPF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IPF 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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ipf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ipf OCA], [http://pdbe.org/6ipf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ipf RCSB], [http://www.ebi.ac.uk/pdbsum/6ipf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ipf 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 ==
		+	Recent research on the structure and mechanism of DNA polymerases has continued to generate fundamentally important features, including a noncanonical pathway involving "prebinding" of metal-bound dNTP (MdNTP) in the absence of DNA. While this noncanonical mechanism was shown to be a possible subset for African swine fever DNA polymerase X (Pol X) and human Pol lambda, it remains unknown whether it could be the primary pathway for a DNA polymerase. Pol mu is a unique member of the X-family with multiple functions and with unusual Mn(2+) preference. Here we report that Pol mu not only prebinds MdNTP in a catalytically active conformation but also exerts a Mn(2+) over Mg(2+) preference at this early stage of catalysis, for various functions: incorporation of dNTP into a single nucleotide gapped DNA, incorporation of rNTP in the nonhomologous end joining (NHEJ) repair, incorporation of dNTP to an ssDNA, and incorporation of an 8-oxo-dGTP opposite template dA (mismatched) or dC (matched). The structural basis of this noncanonical mechanism and Mn(2+) over Mg(2+) preference in these functions was analyzed by solving 19 structures of prebinding binary complexes, precatalytic ternary complexes, and product complexes. The results suggest that the noncanonical pathway is functionally relevant for the multiple functions of Pol mu. Overall, this work provides the structural and mechanistic basis for the long-standing puzzle in the Mn(2+) preference of Pol mu and expands the landscape of the possible mechanisms of DNA polymerases to include both mechanistic pathways.

-	~~Authors~~:	+	Human DNA Polymerase mu Can Use a Noncanonical Mechanism for Multiple Mn(2+)-Mediated Functions.,Chang YK, Huang YP, Liu XX, Ko TP, Bessho Y, Kawano Y, Maestre-Reyna M, Wu WJ, Tsai MD J Am Chem Soc. 2019 May 17. doi: 10.1021/jacs.9b01741. PMID:31067051<ref>PMID:31067051</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6ipf" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
		+	[[Category: Chang, Y K]]
		+	[[Category: Tsai, M D]]
		+	[[Category: Wu, W J]]
		+	[[Category: 8-oxo-dgtp]]
		+	[[Category: Dna break repair]]
		+	[[Category: Dna polymerase mu]]
		+	[[Category: Transferase-dna complex]]

OCA at 05:08, 5 December 2018

2018-12-05T05:08:10Z

←Older revision		Revision as of 05:08, 5 December 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ipf is ON HOLD	+	The entry 6ipf is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6ipf" [edit=sysop:move=sysop]

2018-11-14T06:29:45Z

Protected "6ipf" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:29, 14 November 2018

OCA: New page: '''Unreleased structure''' The entry 6ipf is ON HOLD Authors: Description: Category: Unreleased Structures

2018-11-14T06:29:43Z

New page: '''Unreleased structure''' The entry 6ipf is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6ipf is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]