1jqr - Revision history

OCA at 07:53, 3 April 2024

OCA — Wed, 03 Apr 2024 07:53:56 GMT

←Older revision		Revision as of 07:53, 3 April 2024
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	==NMR structure of the African swine fever virus DNA polymerase X==		==NMR structure of the African swine fever virus DNA polymerase X==
-	<StructureSection load='1jqr' size='340' side='right'caption='[[1jqr~~]], [[NMR_Ensembles_of_Models \| 21 NMR models~~]]' scene=''>	+	<StructureSection load='1jqr' size='340' side='right'caption='[[1jqr]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jqr]] 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=1JQR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JQR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jqr]] 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=1JQR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JQR FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>O174L ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~10497 ASF])~~</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jqr OCA], [https://pdbe.org/1jqr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jqr RCSB], [https://www.ebi.ac.uk/pdbsum/1jqr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jqr 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=1jqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jqr OCA], [https://pdbe.org/1jqr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jqr RCSB], [https://www.ebi.ac.uk/pdbsum/1jqr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jqr 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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 19:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1jqr ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1jqr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The African swine fever virus DNA polymerase X (ASFV Pol X or Pol X), the smallest known nucleotide polymerase, has recently been reported to be an extremely low fidelity polymerase that may be involved in strategic mutagenesis of the viral genome. Here we report the solution structure of Pol X. The structure, unique within the realm of nucleotide polymerases, consists of only palm and fingers subdomains. Despite the absence of a thumb subdomain, which is important for DNA binding in other polymerases, we show that Pol X binds DNA with very high affinity. Further structural analyses suggest a novel mode of DNA binding that may contribute to low fidelity synthesis. We also demonstrate that the ASFV DNA ligase is a low fidelity ligase capable of sealing a nick that contains a G-G mismatch. This supports the hypothesis of a virus-encoded, mutagenic base excision repair pathway consisting of a tandem Pol X/ligase mutator.
-
-	Solution structure of a viral DNA polymerase X and evidence for a mutagenic function.,Showalter AK, Byeon IJ, Su MI, Tsai MD Nat Struct Biol. 2001 Nov;8(11):942-6. PMID:11685239<ref>PMID:11685239</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1jqr" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Asf~~]]	+	[[Category: African swine fever virus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Byeon, I ~~J.L~~]]	+	[[Category: Byeon I-JL]]
-	[[Category: Showalter~~, A K~~]]	+	[[Category: Showalter AK]]
-	[[Category: Su, M I]]	+	[[Category: Su M-I]]
-	[[Category: Tsai, M D]]	+	[[Category: Tsai M-D]]
-	~~[[Category: Dna polymerase]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 08:04, 23 February 2022

OCA — Wed, 23 Feb 2022 08:04:48 GMT

←Older revision		Revision as of 08:04, 23 February 2022
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	<StructureSection load='1jqr' size='340' side='right'caption='[[1jqr]], [[NMR_Ensembles_of_Models \| 21 NMR models]]' scene=''>		<StructureSection load='1jqr' size='340' side='right'caption='[[1jqr]], [[NMR_Ensembles_of_Models \| 21 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jqr]] 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=1JQR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1JQR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jqr]] 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=1JQR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JQR FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">O174L ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10497 ASF])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">O174L ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10497 ASF])</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=1jqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jqr OCA], [~~http~~://pdbe.org/1jqr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1jqr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1jqr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1jqr 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=1jqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jqr OCA], [https://pdbe.org/1jqr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jqr RCSB], [https://www.ebi.ac.uk/pdbsum/1jqr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jqr 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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:34, 25 November 2020

OCA — Wed, 25 Nov 2020 07:34:39 GMT

←Older revision		Revision as of 07:34, 25 November 2020
Line 1:		Line 1:

	==NMR structure of the African swine fever virus DNA polymerase X==		==NMR structure of the African swine fever virus DNA polymerase X==
-	<StructureSection load='1jqr' size='340' side='right' caption='[[1jqr]], [[NMR_Ensembles_of_Models \| 21 NMR models]]' scene=''>	+	<StructureSection load='1jqr' size='340' side='right'caption='[[1jqr]], [[NMR_Ensembles_of_Models \| 21 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jqr]] 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=1JQR OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1JQR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jqr]] 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=1JQR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1JQR FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">O174L ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10497 ASF])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">O174L ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10497 ASF])</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=1jqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jqr OCA], [http://pdbe.org/1jqr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jqr RCSB], [http://www.ebi.ac.uk/pdbsum/1jqr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1jqr 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=1jqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jqr OCA], [http://pdbe.org/1jqr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jqr RCSB], [http://www.ebi.ac.uk/pdbsum/1jqr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1jqr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Asf]]		[[Category: Asf]]
		+	[[Category: Large Structures]]
	[[Category: Byeon, I J.L]]		[[Category: Byeon, I J.L]]
	[[Category: Showalter, A K]]		[[Category: Showalter, A K]]

OCA at 08:42, 17 January 2018

OCA — Wed, 17 Jan 2018 08:42:28 GMT

←Older revision		Revision as of 08:42, 17 January 2018
Line 1:		Line 1:
		+
	==NMR structure of the African swine fever virus DNA polymerase X==		==NMR structure of the African swine fever virus DNA polymerase X==
	<StructureSection load='1jqr' size='340' side='right' caption='[[1jqr]], [[NMR_Ensembles_of_Models \| 21 NMR models]]' scene=''>		<StructureSection load='1jqr' size='340' side='right' caption='[[1jqr]], [[NMR_Ensembles_of_Models \| 21 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1jqr]] 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=1JQR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JQR FirstGlance]. <br>		<table><tr><td colspan='2'>[[1jqr]] 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=1JQR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JQR FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">O174L ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10497 ASF])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">O174L ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10497 ASF])</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=1jqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jqr OCA], [http://pdbe.org/1jqr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jqr RCSB], [http://www.ebi.ac.uk/pdbsum/1jqr 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=1jqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jqr OCA], [http://pdbe.org/1jqr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jqr RCSB], [http://www.ebi.ac.uk/pdbsum/1jqr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1jqr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jq/1jqr_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jq/1jqr_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 27:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1jqr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1jqr" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Methane monooxygenase\|Methane monooxygenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:42, 9 February 2016

OCA — Tue, 09 Feb 2016 21:42:32 GMT

←Older revision		Revision as of 21:42, 9 February 2016
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1jqr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:18, 11 September 2015

OCA — Fri, 11 Sep 2015 02:18:29 GMT

←Older revision		Revision as of 02:18, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1jqr' size='340' side='right' caption='[[1jqr]], [[NMR_Ensembles_of_Models \| 21 NMR models]]' scene=''>		<StructureSection load='1jqr' size='340' side='right' caption='[[1jqr]], [[NMR_Ensembles_of_Models \| 21 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jqr]] is a 1 chain structure with sequence from [http://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=1JQR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JQR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jqr]] 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=1JQR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JQR FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">O174L ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10497 ~~African swine fever virus~~])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">O174L ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10497 ASF])</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=1jqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jqr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jqr RCSB], [http://www.ebi.ac.uk/pdbsum/1jqr 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=1jqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jqr OCA], [http://pdbe.org/1jqr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jqr RCSB], [http://www.ebi.ac.uk/pdbsum/1jqr 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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 24:		Line 26:
	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 1jqr" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 31:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~African swine fever virus~~]]	+	[[Category: Asf]]
	[[Category: Byeon, I J.L]]		[[Category: Byeon, I J.L]]
	[[Category: Showalter, A K]]		[[Category: Showalter, A K]]

OCA at 12:07, 2 January 2015

OCA — Fri, 02 Jan 2015 12:07:07 GMT

←Older revision		Revision as of 12:07, 2 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1jqr]] is a 1 chain structure with sequence from [http://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=1JQR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JQR FirstGlance]. <br>		<table><tr><td colspan='2'>[[1jqr]] is a 1 chain structure with sequence from [http://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=1JQR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JQR FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">O174L ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10497 African swine fever virus])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">O174L ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10497 African swine fever virus])</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=1jqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jqr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jqr RCSB], [http://www.ebi.ac.uk/pdbsum/1jqr 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=1jqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jqr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jqr RCSB], [http://www.ebi.ac.uk/pdbsum/1jqr PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: African swine fever virus]]		[[Category: African swine fever virus]]
-	[[Category: Byeon, I J.L.]]	+	[[Category: Byeon, I J.L]]
-	[[Category: Showalter, A K.]]	+	[[Category: Showalter, A K]]
-	[[Category: Su, M I.]]	+	[[Category: Su, M I]]
-	[[Category: Tsai, M D.]]	+	[[Category: Tsai, M D]]
	[[Category: Dna polymerase]]		[[Category: Dna polymerase]]
	[[Category: Viral protein]]		[[Category: Viral protein]]

OCA at 12:26, 28 September 2014

OCA — Sun, 28 Sep 2014 12:26:10 GMT

←Older revision		Revision as of 12:26, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1jqr.~~png\|left~~\|200px]]	+	==NMR structure of the African swine fever virus DNA polymerase X==
		+	<StructureSection load='1jqr' size='340' side='right' caption='[[1jqr]], [[NMR_Ensembles_of_Models \| 21 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1jqr]] is a 1 chain structure with sequence from [http://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=1JQR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JQR FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">O174L ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10497 African swine fever virus])</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=1jqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jqr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jqr RCSB], [http://www.ebi.ac.uk/pdbsum/1jqr PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jq/1jqr_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The African swine fever virus DNA polymerase X (ASFV Pol X or Pol X), the smallest known nucleotide polymerase, has recently been reported to be an extremely low fidelity polymerase that may be involved in strategic mutagenesis of the viral genome. Here we report the solution structure of Pol X. The structure, unique within the realm of nucleotide polymerases, consists of only palm and fingers subdomains. Despite the absence of a thumb subdomain, which is important for DNA binding in other polymerases, we show that Pol X binds DNA with very high affinity. Further structural analyses suggest a novel mode of DNA binding that may contribute to low fidelity synthesis. We also demonstrate that the ASFV DNA ligase is a low fidelity ligase capable of sealing a nick that contains a G-G mismatch. This supports the hypothesis of a virus-encoded, mutagenic base excision repair pathway consisting of a tandem Pol X/ligase mutator.

-	~~{{STRUCTURE_1jqr\| PDB=1jqr \| SCENE= }}~~	+	Solution structure of a viral DNA polymerase X and evidence for a mutagenic function.,Showalter AK, Byeon IJ, Su MI, Tsai MD Nat Struct Biol. 2001 Nov;8(11):942-6. PMID:11685239<ref>PMID:11685239</ref>

-	~~===NMR structure~~ of the ~~African swine fever virus DNA polymerase X===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_11685239}}~~	+	==See Also==
-		+	*[[Methane monooxygenase\|Methane monooxygenase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1jqr~~]] is a 1 chain structure with sequence from [http://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=1JQR OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:011685239<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: African swine fever virus]]		[[Category: African swine fever virus]]
	[[Category: Byeon, I J.L.]]		[[Category: Byeon, I J.L.]]

OCA: Protected "1jqr" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2012 11:16:40 GMT

Protected "1jqr" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:16, 5 December 2012

OCA at 11:16, 5 December 2012

OCA — Wed, 05 Dec 2012 11:16:39 GMT

←Older revision		Revision as of 11:16, 5 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1jqr.png\|left\|200px]]		[[Image:1jqr.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1jqr", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1jqr\| PDB=1jqr \| SCENE= }}		{{STRUCTURE_1jqr\| PDB=1jqr \| SCENE= }}

	===NMR structure of the African swine fever virus DNA polymerase X===		===NMR structure of the African swine fever virus DNA polymerase X===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11685239}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11685239 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_11685239}}		{{ABSTRACT_PUBMED_11685239}}

	==About this Structure==		==About this Structure==
-	~~1JQR~~ is a 1 chain structure of sequence from [http://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=1JQR OCA].	+	[[1jqr]] is a 1 chain structure with sequence from [http://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=1JQR OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~11685239~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:011685239</ref><references group="xtra"/>
	[[Category: African swine fever virus]]		[[Category: African swine fever virus]]
	[[Category: Byeon, I J.L.]]		[[Category: Byeon, I J.L.]]
Line 30:		Line 18:
	[[Category: Tsai, M D.]]		[[Category: Tsai, M D.]]
	[[Category: Dna polymerase]]		[[Category: Dna polymerase]]
-		+	[[Category: Viral protein]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 12:58:13 2009''~~	+