2far - Revision history

OCA at 09:24, 30 August 2023

2023-08-30T09:24:24Z

← Older revision		Revision as of 09:24, 30 August 2023
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	<StructureSection load='2far' size='340' side='right'caption='[[2far]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2far' size='340' side='right'caption='[[2far]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2far]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FAR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FAR FirstGlance]. <br>		<table><tr><td colspan='2'>[[2far]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FAR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FAR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.9Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2fao\|2fao]], [[2faq\|2faq]]</div~~></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=2far FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2far OCA], [https://pdbe.org/2far PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2far RCSB], [https://www.ebi.ac.uk/pdbsum/2far PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2far 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=2far FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2far OCA], [https://pdbe.org/2far PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2far RCSB], [https://www.ebi.ac.uk/pdbsum/2far PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2far ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/LIGD_PSEAE LIGD_PSEAE] With Ku probably forms a non-homologous end joining (NHEJ) repair enzyme, which repairs dsDNA breaks (DSB) with reduced fidelity. Acts as a DNA ligase on singly nicked dsDNA, fills dsDNA gaps (3- or 4- nucleotide gaps, prefers a 5'-phosphate at the gap distal end, prefers dNTPs over rNTPs) (PubMed:20018881), has DNA-directed DNA polymerase activity (templated primer extension) and DNA-directed RNA polymerase activity (PubMed:15897197), adds 1 or 2 non-templated rNTP (or less well dNTP) to ssDNA or blunt-end dsDNA (primer extension). Has 3' resection activity, removing 3'-rNMPs from DNA using its 3'-ribonuclease and 3'-phosphatase activities sequentially. Resection requires a 2'-OH in the penultimate nucleoside position (i.e. a ribo- not deoxyribonucleoside) (PubMed:15897197), although the 3'-phosphatase activity does not, and its specific activity is 16-fold higher on a DNA substrate (PubMed:16046407). On appropriate substrates will extend a DNA primer to the end of the template strand and then incorporate a non-templated nucleotide.<ref>PMID:15897197</ref> <ref>PMID:16046407</ref> <ref>PMID:20018881</ref> The preference of the polymerase domain for rNTPs over dNTPs may be advantageous in quiescent cells where the dNTP pool may be limiting.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Aniukwu, J]]		[[Category: Pseudomonas aeruginosa]]
	[[Category: Glickman~~, M S~~]]		[[Category: Aniukwu J]]
	[[Category: Lima~~, C D~~]]		[[Category: Glickman MS]]
	[[Category: Nandakumar, J]]		[[Category: Lima CD]]
	[[Category: Shuman, S]]		[[Category: Nandakumar J]]
	[[Category: Wang~~, L K~~]]		[[Category: Shuman S]]
	[[Category: Zhu, H]]		[[Category: Wang LK]]
	~~[[Category: Datp]]~~		[[Category: Zhu H]]
	~~[[Category: Hydrolase-transferase complex]]~~
	~~[[Category: Ligase]]~~
	~~[[Category: Nhej]]~~
	~~[[Category: Polymerase]]~~
	~~[[Category: Primase~~]]

OCA at 09:53, 5 May 2021

2021-05-05T09:53:49Z

← Older revision		Revision as of 09:53, 5 May 2021
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	<StructureSection load='2far' size='340' side='right'caption='[[2far]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2far' size='340' side='right'caption='[[2far]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2far]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FAR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2FAR FirstGlance]. <br>		<table><tr><td colspan='2'>[[2far]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FAR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FAR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fao\|2fao]], [[2faq\|2faq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2fao\|2fao]], [[2faq\|2faq]]</div></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=2far FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2far OCA], [~~http~~://pdbe.org/2far PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2far RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2far PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2far 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=2far FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2far OCA], [https://pdbe.org/2far PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2far RCSB], [https://www.ebi.ac.uk/pdbsum/2far PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2far ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 09:09, 24 July 2019

2019-07-24T09:09:38Z

← Older revision		Revision as of 09:09, 24 July 2019
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	==Crystal Structure of Pseudomonas aeruginosa LigD polymerase domain with dATP and Manganese==		==Crystal Structure of Pseudomonas aeruginosa LigD polymerase domain with dATP and Manganese==
	<StructureSection load='2far' size='340' side='right' caption='[[2far]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2far' size='340' side='right'caption='[[2far]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2far]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FAR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FAR FirstGlance]. <br>		<table><tr><td colspan='2'>[[2far]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FAR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FAR FirstGlance]. <br>
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fa/2far_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fa/2far_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>
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	</div>		</div>
	<div class="pdbe-citations 2far" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2far" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[DNA ligase 3D structures\|DNA ligase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Aniukwu, J]]		[[Category: Aniukwu, J]]
	[[Category: Glickman, M S]]		[[Category: Glickman, M S]]

OCA at 07:36, 18 October 2017

2017-10-18T07:36:19Z

← Older revision		Revision as of 07:36, 18 October 2017
Line 1:		Line 1:

	==Crystal Structure of Pseudomonas aeruginosa LigD polymerase domain with dATP and Manganese==		==Crystal Structure of Pseudomonas aeruginosa LigD polymerase domain with dATP and Manganese==
	<StructureSection load='2far' size='340' side='right' caption='[[2far]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2far' size='340' side='right' caption='[[2far]], [[Resolution\|resolution]] 1.90Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fao\|2fao]], [[2faq\|2faq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fao\|2fao]], [[2faq\|2faq]]</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=2far FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2far OCA], [http://pdbe.org/2far PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2far RCSB], [http://www.ebi.ac.uk/pdbsum/2far 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=2far FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2far OCA], [http://pdbe.org/2far PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2far RCSB], [http://www.ebi.ac.uk/pdbsum/2far PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2far ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</div>		</div>
	<div class="pdbe-citations 2far" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2far" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[DNA ligase\|DNA ligase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 04:17, 9 February 2016

2016-02-09T04:17:07Z

← Older revision		Revision as of 04:17, 9 February 2016
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	<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=2far ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 18:32, 10 September 2015

2015-09-10T18:32:58Z

← Older revision		Revision as of 18:32, 10 September 2015
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	<StructureSection load='2far' size='340' side='right' caption='[[2far]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2far' size='340' side='right' caption='[[2far]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2far]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pseudomonas_aeruginosa Pseudomonas aeruginosa~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FAR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FAR FirstGlance]. <br>		<table><tr><td colspan='2'>[[2far]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FAR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FAR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fao\|2fao]], [[2faq\|2faq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fao\|2fao]], [[2faq\|2faq]]</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=2far FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2far OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2far RCSB], [http://www.ebi.ac.uk/pdbsum/2far 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=2far FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2far OCA], [http://pdbe.org/2far PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2far RCSB], [http://www.ebi.ac.uk/pdbsum/2far PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	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 2far" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Pseudomonas aeruginosa]]~~
	[[Category: Aniukwu, J]]		[[Category: Aniukwu, J]]
	[[Category: Glickman, M S]]		[[Category: Glickman, M S]]

OCA at 09:01, 16 January 2015

2015-01-16T09:01:25Z

← Older revision		Revision as of 09:01, 16 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2far]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FAR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FAR FirstGlance]. <br>		<table><tr><td colspan='2'>[[2far]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FAR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FAR FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fao\|2fao]], [[2faq\|2faq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fao\|2fao]], [[2faq\|2faq]]</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=2far FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2far OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2far RCSB], [http://www.ebi.ac.uk/pdbsum/2far 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=2far FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2far OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2far RCSB], [http://www.ebi.ac.uk/pdbsum/2far PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Pseudomonas aeruginosa]]		[[Category: Pseudomonas aeruginosa]]
	[[Category: Aniukwu, J.]]		[[Category: Aniukwu, J]]
	[[Category: Glickman, M S.]]		[[Category: Glickman, M S]]
	[[Category: Lima, C D.]]		[[Category: Lima, C D]]
	[[Category: Nandakumar, J.]]		[[Category: Nandakumar, J]]
	[[Category: Shuman, S.]]		[[Category: Shuman, S]]
	[[Category: Wang, L K.]]		[[Category: Wang, L K]]
	[[Category: Zhu, H.]]		[[Category: Zhu, H]]
	[[Category: Datp]]		[[Category: Datp]]
	[[Category: Hydrolase-transferase complex]]		[[Category: Hydrolase-transferase complex]]

OCA at 03:59, 29 September 2014

2014-09-29T03:59:36Z

← Older revision		Revision as of 03:59, 29 September 2014
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	[[Image:~~2far~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal Structure of Pseudomonas aeruginosa LigD polymerase domain with dATP and Manganese==
			<StructureSection load='2far' size='340' side='right' caption='[[2far]], [[Resolution\|resolution]] 1.90Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2far]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FAR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FAR FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fao\|2fao]], [[2faq\|2faq]]</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=2far FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2far OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2far RCSB], [http://www.ebi.ac.uk/pdbsum/2far 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/fa/2far_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 ==
			DNA ligase D (LigD) is a large polyfunctional protein that participates in a recently discovered pathway of nonhomologous end-joining in bacteria. LigD consists of an ATP-dependent ligase domain fused to a polymerase domain (Pol) and a phosphoesterase module. The Pol activity is remarkable for its dependence on manganese, its ability to perform templated and nontemplated primer extension reactions, and its preference for adding ribonucleotides to blunt DNA ends. Here we report the 1.5-A crystal structure of the Pol domain of Pseudomonas LigD and its complexes with manganese and ATP/dATP substrates, which reveal a minimized polymerase with a two-metal mechanism and a fold similar to that of archaeal DNA primase. Mutational analysis highlights the functionally relevant atomic contacts in the active site. Although distinct nucleoside conformations and contacts for ATP versus dATP are observed in the cocrystals, the functional analysis suggests that the ATP-binding mode is the productive conformation for dNMP and rNMP incorporation. We find that a mutation of Mycobacterium LigD that uniquely ablates the polymerase activity results in increased fidelity of blunt-end double-strand break repair in vivo by virtue of eliminating nucleotide insertions at the recombination junctions. Thus, LigD Pol is a direct catalyst of mutagenic nonhomologous end-joining in vivo. Our studies underscore a previously uncharacterized role for the primase-like polymerase family in DNA repair.

	~~{{STRUCTURE_2far\| PDB=2far \| SCENE= }}~~		Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D.,Zhu H, Nandakumar J, Aniukwu J, Wang LK, Glickman MS, Lima CD, Shuman S Proc Natl Acad Sci U S A. 2006 Feb 7;103(6):1711-6. Epub 2006 Jan 30. PMID:16446439<ref>PMID:16446439</ref>

	~~===Crystal Structure~~ of ~~Pseudomonas aeruginosa LigD polymerase domain with dATP and Manganese===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16446439}}~~

	~~==About this Structure==~~
	~~[[2far]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]~~. ~~Full crystallographic information is available from [http://oca.weizmann.ac.il~~/~~oca-bin/ocashort?id=2FAR OCA].~~

	==See Also==		==See Also==
	*[[DNA ligase\|DNA ligase]]		*[[DNA ligase\|DNA ligase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:016446439<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Pseudomonas aeruginosa]]		[[Category: Pseudomonas aeruginosa]]
	[[Category: Aniukwu, J.]]		[[Category: Aniukwu, J.]]

OCA at 12:37, 20 October 2012

2012-10-20T12:37:06Z

← Older revision		Revision as of 12:37, 20 October 2012
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	==About this Structure==		==About this Structure==
	[[2far]] is a 2 chain structure ~~of [[DNA ligase]]~~ with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FAR OCA].		[[2far]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FAR OCA].

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

OCA at 09:19, 26 July 2012

2012-07-26T09:19:05Z

← Older revision		Revision as of 09:19, 26 July 2012
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	[[Image:2far.png\|left\|200px]]		[[Image:2far.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2far", 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_2far\| PDB=2far \| SCENE= }}		{{STRUCTURE_2far\| PDB=2far \| SCENE= }}

	===Crystal Structure of Pseudomonas aeruginosa LigD polymerase domain with dATP and Manganese===		===Crystal Structure of Pseudomonas aeruginosa LigD polymerase domain with dATP and Manganese===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_16446439}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 16446439 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_16446439}}		{{ABSTRACT_PUBMED_16446439}}

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	==See Also==		==See Also==
	*[[DNA ligase]]		*[[DNA ligase\|DNA ligase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~16446439~~</ref><references group="xtra"/>		<ref group="xtra">PMID:016446439</ref><references group="xtra"/>
	[[Category: Pseudomonas aeruginosa]]		[[Category: Pseudomonas aeruginosa]]
	[[Category: Aniukwu, J.]]		[[Category: Aniukwu, J.]]
Line 35:		Line 24:
	[[Category: Zhu, H.]]		[[Category: Zhu, H.]]
	[[Category: Datp]]		[[Category: Datp]]
	[[Category: Hydrolase/transferase complex]]		[[Category: Hydrolase-transferase complex]]
	[[Category: Ligase]]		[[Category: Ligase]]
	[[Category: Nhej]]		[[Category: Nhej]]
	[[Category: Polymerase]]		[[Category: Polymerase]]
	[[Category: Primase]]		[[Category: Primase]]