2m2u - Revision history

OCA at 06:58, 1 May 2024

2024-05-01T06:58:44Z

←Older revision		Revision as of 06:58, 1 May 2024
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	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/DPOLX_ASFB7 DPOLX_ASFB7] Error-prone polymerase lacking a proofreading 3'-5' exonuclease which plays a role in viral DNA repair. Specifically binds intermediates in the single-nucleotide base-excision repair process. Also catalyzes DNA polymerization with low nucleotide-insertion fidelity. Together with the viral DNA ligase, fills the single nucleotide gaps generated by the AP endonuclease.<ref>PMID:12595253</ref> <ref>PMID:11685239</ref>		[https://www.uniprot.org/uniprot/DPOLX_ASFB7 DPOLX_ASFB7] Error-prone polymerase lacking a proofreading 3'-5' exonuclease which plays a role in viral DNA repair. Specifically binds intermediates in the single-nucleotide base-excision repair process. Also catalyzes DNA polymerization with low nucleotide-insertion fidelity. Together with the viral DNA ligase, fills the single nucleotide gaps generated by the AP endonuclease.<ref>PMID:12595253</ref> <ref>PMID:11685239</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	A dogma for DNA polymerase catalysis is that the enzyme binds DNA first, followed by MgdNTP. This mechanism contributes to the selection of correct dNTP by Watson-Crick base pairing, but it cannot explain how low-fidelity DNA polymerases overcome Watson-Crick base pairing to catalyze non-Watson-Crick dNTP incorporation. DNA polymerase X from the deadly African swine fever virus (Pol X) is a half-sized repair polymerase that catalyzes efficient dG:dGTP incorporation in addition to correct repair. Here we report the use of solution structures of Pol X in the free, binary (Pol X:MgdGTP), and ternary (Pol X:DNA:MgdGTP with dG:dGTP non-Watson-Crick pairing) forms, along with functional analyses, to show that Pol X uses multiple unprecedented strategies to achieve the mutagenic dG:dGTP incorporation. Unlike high fidelity polymerases, Pol X can prebind purine MgdNTP tightly and undergo a specific conformational change in the absence of DNA. The prebound MgdGTP assumes an unusual syn conformation stabilized by partial ring stacking with His115. Upon binding of a gapped DNA, also with a unique mechanism involving primarily helix alphaE, the prebound syn-dGTP forms a Hoogsteen base pair with the template anti-dG. Interestingly, while Pol X prebinds MgdCTP weakly, the correct dG:dCTP ternary complex is readily formed in the presence of DNA. H115A mutation disrupted MgdGTP binding and dG:dGTP ternary complex formation but not dG:dCTP ternary complex formation. The results demonstrate the first solution structural view of DNA polymerase catalysis, a unique DNA binding mode, and a novel mechanism for non-Watson-Crick incorporation by a low-fidelity DNA polymerase.
-
-	How a Low-Fidelity DNA Polymerase Chooses Non-Watson-Crick from Watson-Crick Incorporation.,Wu WJ, Su MI, Wu JL, Kumar S, Lim LH, Wang CW, Nelissen FH, Chen MC, Doreleijers JF, Wijmenga SS, Tsai MD J Am Chem Soc. 2014 Mar 21. PMID:24617852<ref>PMID:24617852</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2m2u" style="background-color:#fffaf0;"></div>

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

OCA at 11:52, 22 November 2023

2023-11-22T11:52:31Z

←Older revision		Revision as of 11:52, 22 November 2023
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	==Binary complex of African Swine Fever Virus Pol X with MgdGTP==		==Binary complex of African Swine Fever Virus Pol X with MgdGTP==
-	<StructureSection load='2m2u' size='340' side='right'caption='[[2m2u~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='2m2u' size='340' side='right'caption='[[2m2u]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2m2u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Asf Asf~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M2U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2M2U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2m2u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/African_swine_fever_virus African swine fever virus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M2U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2M2U FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[2m2t\|2m2t]], [[2m2v\|2m2v]], [[2m2w\|2m2w]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://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=2m2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m2u OCA], [https://pdbe.org/2m2u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2m2u RCSB], [https://www.ebi.ac.uk/pdbsum/2m2u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2m2u 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=2m2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m2u OCA], [https://pdbe.org/2m2u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2m2u RCSB], [https://www.ebi.ac.uk/pdbsum/2m2u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2m2u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DPOLX_ASFB7 DPOLX_ASFB7]] Error-prone polymerase lacking a proofreading 3'-5' exonuclease which plays a role in viral DNA repair. Specifically binds intermediates in the single-nucleotide base-excision repair process. Also catalyzes DNA polymerization with low nucleotide-insertion fidelity. Together with the viral DNA ligase, fills the single nucleotide gaps generated by the AP endonuclease.<ref>PMID:12595253</ref> <ref>PMID:11685239</ref>	+	[https://www.uniprot.org/uniprot/DPOLX_ASFB7 DPOLX_ASFB7] Error-prone polymerase lacking a proofreading 3'-5' exonuclease which plays a role in viral DNA repair. Specifically binds intermediates in the single-nucleotide base-excision repair process. Also catalyzes DNA polymerization with low nucleotide-insertion fidelity. Together with the viral DNA ligase, fills the single nucleotide gaps generated by the AP endonuclease.<ref>PMID:12595253</ref> <ref>PMID:11685239</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 2m2u" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2m2u" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Asf]]~~	+	[[Category: African swine fever virus]]
-	~~[[Category: DNA-directed DNA polymerase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Su, M]]	+	[[Category: Su M]]
-	[[Category: Tsai, M]]	+	[[Category: Tsai M]]
-	[[Category: Wu, W]]	+	[[Category: Wu W]]
-	~~[[Category: Dna polymerase]]~~	+
-	~~[[Category: Nucleotidyl transferase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 11:32, 16 February 2022

2022-02-16T11:32:04Z

←Older revision		Revision as of 11:32, 16 February 2022
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	<StructureSection load='2m2u' size='340' side='right'caption='[[2m2u]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2m2u' size='340' side='right'caption='[[2m2u]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2m2u]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Asf Asf]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M2U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2M2U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2m2u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Asf Asf]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M2U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2M2U FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2m2t\|2m2t]], [[2m2v\|2m2v]], [[2m2w\|2m2w]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2m2t\|2m2t]], [[2m2v\|2m2v]], [[2m2w\|2m2w]]</div></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'>[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://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~~://proteopedia.org/fgij/fg.htm?mol=2m2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m2u OCA], [~~http~~://pdbe.org/2m2u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2m2u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2m2u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2m2u 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=2m2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m2u OCA], [https://pdbe.org/2m2u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2m2u RCSB], [https://www.ebi.ac.uk/pdbsum/2m2u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2m2u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DPOLX_ASFB7 DPOLX_ASFB7]] Error-prone polymerase lacking a proofreading 3'-5' exonuclease which plays a role in viral DNA repair. Specifically binds intermediates in the single-nucleotide base-excision repair process. Also catalyzes DNA polymerization with low nucleotide-insertion fidelity. Together with the viral DNA ligase, fills the single nucleotide gaps generated by the AP endonuclease.<ref>PMID:12595253</ref> <ref>PMID:11685239</ref>	+	[[https://www.uniprot.org/uniprot/DPOLX_ASFB7 DPOLX_ASFB7]] Error-prone polymerase lacking a proofreading 3'-5' exonuclease which plays a role in viral DNA repair. Specifically binds intermediates in the single-nucleotide base-excision repair process. Also catalyzes DNA polymerization with low nucleotide-insertion fidelity. Together with the viral DNA ligase, fills the single nucleotide gaps generated by the AP endonuclease.<ref>PMID:12595253</ref> <ref>PMID:11685239</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 2m2u" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2m2u" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:18, 13 May 2020

2020-05-13T06:18:17Z

←Older revision		Revision as of 06:18, 13 May 2020
Line 1:		Line 1:

	==Binary complex of African Swine Fever Virus Pol X with MgdGTP==		==Binary complex of African Swine Fever Virus Pol X with MgdGTP==
-	<StructureSection load='2m2u' size='340' side='right' caption='[[2m2u]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='2m2u' size='340' side='right'caption='[[2m2u]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2m2u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Asf Asf]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M2U OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2M2U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2m2u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Asf Asf]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M2U OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2M2U FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2m2t\|2m2t]], [[2m2v\|2m2v]], [[2m2w\|2m2w]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2m2t\|2m2t]], [[2m2v\|2m2v]], [[2m2w\|2m2w]]</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=2m2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m2u OCA], [http://pdbe.org/2m2u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2m2u RCSB], [http://www.ebi.ac.uk/pdbsum/2m2u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2m2u 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=2m2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m2u OCA], [http://pdbe.org/2m2u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2m2u RCSB], [http://www.ebi.ac.uk/pdbsum/2m2u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2m2u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 2m2u" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2m2u" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 26:		Line 29:
	[[Category: Asf]]		[[Category: Asf]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Su, M]]		[[Category: Su, M]]
	[[Category: Tsai, M]]		[[Category: Tsai, M]]

OCA at 22:52, 9 August 2018

2018-08-09T22:52:59Z

←Older revision		Revision as of 22:52, 9 August 2018
Line 1:		Line 1:
		+
	==Binary complex of African Swine Fever Virus Pol X with MgdGTP==		==Binary complex of African Swine Fever Virus Pol X with MgdGTP==
	<StructureSection load='2m2u' size='340' side='right' caption='[[2m2u]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2m2u' size='340' side='right' caption='[[2m2u]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2m2t\|2m2t]], [[2m2v\|2m2v]], [[2m2w\|2m2w]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2m2t\|2m2t]], [[2m2v\|2m2v]], [[2m2w\|2m2w]]</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=2m2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m2u OCA], [http://pdbe.org/2m2u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2m2u RCSB], [http://www.ebi.ac.uk/pdbsum/2m2u 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=2m2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m2u OCA], [http://pdbe.org/2m2u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2m2u RCSB], [http://www.ebi.ac.uk/pdbsum/2m2u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2m2u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 2m2u" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2m2u" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 23:08, 11 September 2015

2015-09-11T23:08:09Z

←Older revision		Revision as of 23:08, 11 September 2015
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2m2t\|2m2t]], [[2m2v\|2m2v]], [[2m2w\|2m2w]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2m2t\|2m2t]], [[2m2v\|2m2v]], [[2m2w\|2m2w]]</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=2m2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m2u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2m2u RCSB], [http://www.ebi.ac.uk/pdbsum/2m2u 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=2m2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m2u OCA], [http://pdbe.org/2m2u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2m2u RCSB], [http://www.ebi.ac.uk/pdbsum/2m2u PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	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 2m2u" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:39, 25 December 2014

2014-12-25T20:39:32Z

←Older revision		Revision as of 20:39, 25 December 2014
Line 2:		Line 2:
	<StructureSection load='2m2u' size='340' side='right' caption='[[2m2u]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2m2u' size='340' side='right' caption='[[2m2u]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2m2u]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M2U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2M2U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2m2u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Asf Asf]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M2U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2M2U FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2m2t\|2m2t]], [[2m2v\|2m2v]], [[2m2w\|2m2w]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2m2t\|2m2t]], [[2m2v\|2m2v]], [[2m2w\|2m2w]]</td></tr>
Line 8:		Line 8:
	<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=2m2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m2u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2m2u RCSB], [http://www.ebi.ac.uk/pdbsum/2m2u 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=2m2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m2u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2m2u RCSB], [http://www.ebi.ac.uk/pdbsum/2m2u PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPOLX_ASFB7 DPOLX_ASFB7]] Error-prone polymerase lacking a proofreading 3'-5' exonuclease which plays a role in viral DNA repair. Specifically binds intermediates in the single-nucleotide base-excision repair process. Also catalyzes DNA polymerization with low nucleotide-insertion fidelity. Together with the viral DNA ligase, fills the single nucleotide gaps generated by the AP endonuclease.<ref>PMID:12595253</ref> <ref>PMID:11685239</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Asf]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Su, M]]		[[Category: Su, M]]

OCA at 07:18, 12 November 2014

2014-11-12T07:18:25Z

←Older revision		Revision as of 07:18, 12 November 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2m2u\| PDB=2m2u \| SCENE= }}~~	+	==Binary complex of African Swine Fever Virus Pol X with MgdGTP==
-	===Binary complex of African Swine Fever Virus Pol X with MgdGTP===	+	<StructureSection load='2m2u' size='340' side='right' caption='[[2m2u]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
-	~~{{ABSTRACT_PUBMED_24617852}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2m2u]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M2U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2M2U FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2m2t\|2m2t]], [[2m2v\|2m2v]], [[2m2w\|2m2w]]</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=2m2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m2u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2m2u RCSB], [http://www.ebi.ac.uk/pdbsum/2m2u PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A dogma for DNA polymerase catalysis is that the enzyme binds DNA first, followed by MgdNTP. This mechanism contributes to the selection of correct dNTP by Watson-Crick base pairing, but it cannot explain how low-fidelity DNA polymerases overcome Watson-Crick base pairing to catalyze non-Watson-Crick dNTP incorporation. DNA polymerase X from the deadly African swine fever virus (Pol X) is a half-sized repair polymerase that catalyzes efficient dG:dGTP incorporation in addition to correct repair. Here we report the use of solution structures of Pol X in the free, binary (Pol X:MgdGTP), and ternary (Pol X:DNA:MgdGTP with dG:dGTP non-Watson-Crick pairing) forms, along with functional analyses, to show that Pol X uses multiple unprecedented strategies to achieve the mutagenic dG:dGTP incorporation. Unlike high fidelity polymerases, Pol X can prebind purine MgdNTP tightly and undergo a specific conformational change in the absence of DNA. The prebound MgdGTP assumes an unusual syn conformation stabilized by partial ring stacking with His115. Upon binding of a gapped DNA, also with a unique mechanism involving primarily helix alphaE, the prebound syn-dGTP forms a Hoogsteen base pair with the template anti-dG. Interestingly, while Pol X prebinds MgdCTP weakly, the correct dG:dCTP ternary complex is readily formed in the presence of DNA. H115A mutation disrupted MgdGTP binding and dG:dGTP ternary complex formation but not dG:dCTP ternary complex formation. The results demonstrate the first solution structural view of DNA polymerase catalysis, a unique DNA binding mode, and a novel mechanism for non-Watson-Crick incorporation by a low-fidelity DNA polymerase.

-	~~==Function==~~	+	How a Low-Fidelity DNA Polymerase Chooses Non-Watson-Crick from Watson-Crick Incorporation.,Wu WJ, Su MI, Wu JL, Kumar S, Lim LH, Wang CW, Nelissen FH, Chen MC, Doreleijers JF, Wijmenga SS, Tsai MD J Am Chem Soc. 2014 Mar 21. PMID:24617852<ref>PMID:24617852</ref>
-	~~[[http://www.uniprot.org/uniprot/DPOLX_ASFB7 DPOLX_ASFB7]] Error-prone polymerase lacking~~ a ~~proofreading 3'~~-~~5' exonuclease which plays a role in viral~~ DNA ~~repair. Specifically binds intermediates in the single~~-~~nucleotide base~~-~~excision repair process. Also catalyzes DNA polymerization with low nucleotide~~-~~insertion fidelity~~. ~~Together with the viral DNA ligase~~, ~~fills the single nucleotide gaps generated by the AP endonuclease~~.~~<ref>~~PMID:~~12595253</ref>~~ <ref>PMID:~~11685239~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[2m2u]] is~~ a ~~1 chain structure~~. ~~Full experimental information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=2M2U OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:024617852</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: Su, M.]]	+	[[Category: Su, M]]
-	[[Category: Tsai, M.]]	+	[[Category: Tsai, M]]
-	[[Category: Wu, W.]]	+	[[Category: Wu, W]]
	[[Category: Dna polymerase]]		[[Category: Dna polymerase]]
	[[Category: Nucleotidyl transferase]]		[[Category: Nucleotidyl transferase]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 09:25, 2 April 2014

2014-04-02T09:25:54Z

←Older revision		Revision as of 09:25, 2 April 2014
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_2m2u\| PDB=2m2u \| SCENE= }}
		+	===Binary complex of African Swine Fever Virus Pol X with MgdGTP===
		+	{{ABSTRACT_PUBMED_24617852}}

-	~~The entry 2m2u is ON HOLD~~ ~~until Apr 03 2015~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/DPOLX_ASFB7 DPOLX_ASFB7]] Error-prone polymerase lacking a proofreading 3'-5' exonuclease which plays a role in viral DNA repair. Specifically binds intermediates in the single-nucleotide base-excision repair process. Also catalyzes DNA polymerization with low nucleotide-insertion fidelity. Together with the viral DNA ligase, fills the single nucleotide gaps generated by the AP endonuclease.<ref>PMID:12595253</ref> <ref>PMID:11685239</ref>

-	~~Authors~~: ~~Wu, W~~.~~, Su, M~~.~~, Tsai, M~~.	+	==About this Structure==
		+	[[2m2u]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M2U OCA].

-	~~Description~~: ~~Binary complex of African Swine Fever Virus Pol X with MgdGTP~~	+	==Reference==
		+	<ref group="xtra">PMID:024617852</ref><references group="xtra"/><references/>
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Su, M.]]
		+	[[Category: Tsai, M.]]
		+	[[Category: Wu, W.]]
		+	[[Category: Dna polymerase]]
		+	[[Category: Nucleotidyl transferase]]
		+	[[Category: Transferase]]

OCA at 08:36, 18 December 2013

2013-12-18T08:36:08Z

←Older revision		Revision as of 08:36, 18 December 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 2m2u is ON HOLD until ~~Paper Publication~~	+	The entry 2m2u is ON HOLD until Apr 03 2015

	Authors: Wu, W., Su, M., Tsai, M.		Authors: Wu, W., Su, M., Tsai, M.

	Description: Binary complex of African Swine Fever Virus Pol X with MgdGTP		Description: Binary complex of African Swine Fever Virus Pol X with MgdGTP