1v9p - Revision history

OCA at 00:00, 28 December 2023

OCA — Thu, 28 Dec 2023 00:00:20 GMT

←Older revision		Revision as of 00:00, 28 December 2023
Line 3:		Line 3:
	<StructureSection load='1v9p' size='340' side='right'caption='[[1v9p]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='1v9p' size='340' side='right'caption='[[1v9p]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1v9p]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_43280 Atcc 43280~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dgt 1dgt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1V9P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1v9p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_filiformis Thermus filiformis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dgt 1dgt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V9P FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>~~, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.9Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1dgt\|1dgt]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>LIGA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~276 ATCC 43280])</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=1v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9p OCA], [https://pdbe.org/1v9p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v9p RCSB], [https://www.ebi.ac.uk/pdbsum/1v9p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v9p ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/DNA_ligase_(NAD(+)) DNA ligase (NAD(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.2 6.5.1.2]~~ </~~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=1v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9p OCA], [~~http~~://pdbe.org/1v9p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1v9p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1v9p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1v9p ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DNLJ_THEFI DNLJ_THEFI]] DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.<ref>PMID:15268945</ref>	+	[https://www.uniprot.org/uniprot/DNLJ_THEFI DNLJ_THEFI] DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.<ref>PMID:15268945</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 43280]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chang, C]]	+	[[Category: Thermus filiformis]]
-	[[Category: Kim~~, H K~~]]	+	[[Category: Chang C]]
-	[[Category: Kwon~~, S K~~]]	+	[[Category: Kim HK]]
-	[[Category: Lee~~, J Y~~]]	+	[[Category: Kwon SK]]
-	[[Category: Moon, J]]	+	[[Category: Lee JY]]
-	[[Category: Song~~, H K~~]]	+	[[Category: Moon J]]
-	[[Category: Suh~~, S W~~]]	+	[[Category: Song HK]]
-	[[Category: Yang~~, J K]]~~	+	[[Category: Suh SW]]
-	~~[[Category: Ligase]]~~	+	[[Category: Yang JK]]
-	~~[[Category: Nad+-dependent dna ligase~~]]	+

OCA at 07:33, 30 December 2020

OCA — Wed, 30 Dec 2020 07:33:47 GMT

←Older revision		Revision as of 07:33, 30 December 2020
Line 1:		Line 1:

	==Crystal Structure Of Nad+-Dependent DNA Ligase==		==Crystal Structure Of Nad+-Dependent DNA Ligase==
-	<StructureSection load='1v9p' size='340' side='right' caption='[[1v9p]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='1v9p' size='340' side='right'caption='[[1v9p]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1v9p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43280 Atcc 43280]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dgt 1dgt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9P OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1V9P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1v9p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43280 Atcc 43280]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dgt 1dgt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1V9P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dgt\|1dgt]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dgt\|1dgt]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LIGA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=276 ATCC 43280])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LIGA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=276 ATCC 43280])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_ligase_(NAD(+)) DNA ligase (NAD(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.2 6.5.1.2] </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_ligase_(NAD(+)) DNA ligase (NAD(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.2 6.5.1.2] </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=1v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9p OCA], [http://pdbe.org/1v9p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1v9p RCSB], [http://www.ebi.ac.uk/pdbsum/1v9p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1v9p 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=1v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9p OCA], [http://pdbe.org/1v9p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1v9p RCSB], [http://www.ebi.ac.uk/pdbsum/1v9p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1v9p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 33:		Line 33:

	==See Also==		==See Also==
-	*[[DNA ligase\|DNA ligase]]	+	*[[DNA ligase 3D structures\|DNA ligase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 43280]]		[[Category: Atcc 43280]]
		+	[[Category: Large Structures]]
	[[Category: Chang, C]]		[[Category: Chang, C]]
	[[Category: Kim, H K]]		[[Category: Kim, H K]]

OCA at 07:25, 4 April 2018

OCA — Wed, 04 Apr 2018 07:25:00 GMT

←Older revision		Revision as of 07:25, 4 April 2018
Line 1:		Line 1:
		+
	==Crystal Structure Of Nad+-Dependent DNA Ligase==		==Crystal Structure Of Nad+-Dependent DNA Ligase==
	<StructureSection load='1v9p' size='340' side='right' caption='[[1v9p]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='1v9p' size='340' side='right' caption='[[1v9p]], [[Resolution\|resolution]] 2.90Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LIGA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=276 ATCC 43280])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LIGA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=276 ATCC 43280])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_ligase_(NAD(+)) DNA ligase (NAD(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.2 6.5.1.2] </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_ligase_(NAD(+)) DNA ligase (NAD(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.2 6.5.1.2] </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=1v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9p OCA], [http://pdbe.org/1v9p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1v9p RCSB], [http://www.ebi.ac.uk/pdbsum/1v9p 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=1v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9p OCA], [http://pdbe.org/1v9p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1v9p RCSB], [http://www.ebi.ac.uk/pdbsum/1v9p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1v9p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v9/1v9p_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v9/1v9p_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>
	</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=1v9p ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:11, 11 September 2015

OCA — Fri, 11 Sep 2015 09:11:50 GMT

←Older revision		Revision as of 09:11, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1v9p' size='340' side='right' caption='[[1v9p]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='1v9p' size='340' side='right' caption='[[1v9p]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1v9p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_filiformis Thermus filiformis~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dgt 1dgt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V9P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1v9p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43280 Atcc 43280]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dgt 1dgt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V9P FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dgt\|1dgt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dgt\|1dgt]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LIGA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=276 ~~Thermus filiformis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LIGA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=276 ATCC 43280])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_ligase_(NAD(+)) DNA ligase (NAD(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.2 6.5.1.2] </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_ligase_(NAD(+)) DNA ligase (NAD(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.2 6.5.1.2] </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=1v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1v9p RCSB], [http://www.ebi.ac.uk/pdbsum/1v9p 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=1v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9p OCA], [http://pdbe.org/1v9p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1v9p RCSB], [http://www.ebi.ac.uk/pdbsum/1v9p PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 1v9p" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Thermus filiformis~~]]	+	[[Category: Atcc 43280]]
	[[Category: Chang, C]]		[[Category: Chang, C]]
	[[Category: Kim, H K]]		[[Category: Kim, H K]]

OCA at 14:19, 25 December 2014

OCA — Thu, 25 Dec 2014 14:19:37 GMT

←Older revision		Revision as of 14:19, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1v9p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_filiformis Thermus filiformis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dgt 1dgt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V9P FirstGlance]. <br>		<table><tr><td colspan='2'>[[1v9p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_filiformis Thermus filiformis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dgt 1dgt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V9P FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dgt\|1dgt]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dgt\|1dgt]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LIGA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=276 Thermus filiformis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LIGA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=276 Thermus filiformis])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_ligase_(NAD(+)) DNA ligase (NAD(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.2 6.5.1.2] </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_ligase_(NAD(+)) DNA ligase (NAD(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.2 6.5.1.2] </span></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=1v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1v9p RCSB], [http://www.ebi.ac.uk/pdbsum/1v9p 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=1v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1v9p RCSB], [http://www.ebi.ac.uk/pdbsum/1v9p PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DNLJ_THEFI DNLJ_THEFI]] DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.<ref>PMID:15268945</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Thermus filiformis]]		[[Category: Thermus filiformis]]
-	[[Category: Chang, C.]]	+	[[Category: Chang, C]]
-	[[Category: Kim, H K.]]	+	[[Category: Kim, H K]]
-	[[Category: Kwon, S K.]]	+	[[Category: Kwon, S K]]
-	[[Category: Lee, J Y.]]	+	[[Category: Lee, J Y]]
-	[[Category: Moon, J.]]	+	[[Category: Moon, J]]
-	[[Category: Song, H K.]]	+	[[Category: Song, H K]]
-	[[Category: Suh, S W.]]	+	[[Category: Suh, S W]]
-	[[Category: Yang, J K.]]	+	[[Category: Yang, J K]]
	[[Category: Ligase]]		[[Category: Ligase]]
	[[Category: Nad+-dependent dna ligase]]		[[Category: Nad+-dependent dna ligase]]

OCA at 23:20, 28 September 2014

OCA — Sun, 28 Sep 2014 23:20:31 GMT

←Older revision		Revision as of 23:20, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1v9p.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure Of Nad+-Dependent DNA Ligase==
		+	<StructureSection load='1v9p' size='340' side='right' caption='[[1v9p]], [[Resolution\|resolution]] 2.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1v9p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_filiformis Thermus filiformis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dgt 1dgt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V9P FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dgt\|1dgt]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LIGA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=276 Thermus filiformis])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_ligase_(NAD(+)) DNA ligase (NAD(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.2 6.5.1.2] </span></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=1v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1v9p RCSB], [http://www.ebi.ac.uk/pdbsum/1v9p 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/v9/1v9p_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 ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor. Despite the difference in cofactor specificity and limited overall sequence similarity, the two classes of DNA ligase share basically the same catalytic mechanism. In this study, the crystal structure of an NAD(+)-dependent DNA ligase from Thermus filiformis, a 667 residue multidomain protein, has been determined by the multiwavelength anomalous diffraction (MAD) method. It reveals highly modular architecture and a unique circular arrangement of its four distinct domains. It also provides clues for protein flexibility and DNA-binding sites. A model for the multidomain ligase action involving large conformational changes is proposed.

-	~~{{STRUCTURE_1v9p\| PDB=1v9p \| SCENE= }}~~	+	Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications.,Lee JY, Chang C, Song HK, Moon J, Yang JK, Kim HK, Kwon ST, Suh SW EMBO J. 2000 Mar 1;19(5):1119-29. PMID:10698952<ref>PMID:10698952</ref>

-	~~===Crystal Structure Of Nad+-Dependent DNA Ligase===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10698952}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1v9p]] is~~ a ~~2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_filiformis Thermus filiformis]. This structure supersedes~~ the ~~now removed PDB entry [http://oca~~.~~weizmann~~.ac.il/~~oca-bin/send-pdb?obs=1&id=1dgt 1dgt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9P OCA].~~	+

	==See Also==		==See Also==
	*[[DNA ligase\|DNA ligase]]		*[[DNA ligase\|DNA ligase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:010698952<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Thermus filiformis]]		[[Category: Thermus filiformis]]
	[[Category: Chang, C.]]		[[Category: Chang, C.]]

OCA at 17:44, 20 October 2012

OCA — Sat, 20 Oct 2012 17:44:32 GMT

←Older revision		Revision as of 17:44, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1v9p]] is a 2 chain structure ~~of [[DNA ligase]]~~ with sequence from [http://en.wikipedia.org/wiki/Thermus_filiformis Thermus filiformis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dgt 1dgt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9P OCA].	+	[[1v9p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_filiformis Thermus filiformis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dgt 1dgt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9P OCA].

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

OCA: Protected "1v9p" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 01:51:02 GMT

Protected "1v9p" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:51, 27 July 2012

OCA at 01:50, 27 July 2012

OCA — Fri, 27 Jul 2012 01:50:59 GMT

←Older revision		Revision as of 01:50, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1v9p.png\|left\|200px]]		[[Image:1v9p.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1v9p", 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_1v9p\| PDB=1v9p \| SCENE= }}		{{STRUCTURE_1v9p\| PDB=1v9p \| SCENE= }}

	===Crystal Structure Of Nad+-Dependent DNA Ligase===		===Crystal Structure Of Nad+-Dependent DNA Ligase===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_10698952}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 10698952 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_10698952}}		{{ABSTRACT_PUBMED_10698952}}

	==About this Structure==		==About this Structure==
-	~~1V9P~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Thermus_filiformis Thermus filiformis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dgt 1dgt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9P OCA].	+	[[1v9p]] is a 2 chain structure of [[DNA ligase]] with sequence from [http://en.wikipedia.org/wiki/Thermus_filiformis Thermus filiformis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dgt 1dgt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9P OCA].
		+
		+	==See Also==
		+	*[[DNA ligase\|DNA ligase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~10698952~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:010698952</ref><references group="xtra"/>
	[[Category: Thermus filiformis]]		[[Category: Thermus filiformis]]
	[[Category: Chang, C.]]		[[Category: Chang, C.]]
Line 33:		Line 24:
	[[Category: Suh, S W.]]		[[Category: Suh, S W.]]
	[[Category: Yang, J K.]]		[[Category: Yang, J K.]]
		+	[[Category: Ligase]]
	[[Category: Nad+-dependent dna ligase]]		[[Category: Nad+-dependent dna ligase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:30:29 2009''

OCA at 16:30, 17 February 2009

OCA — Tue, 17 Feb 2009 16:30:31 GMT

←Older revision		Revision as of 16:30, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1V9P is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Thermus_filiformis Thermus filiformis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dgt 1dgt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9P OCA].	+	1V9P is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Thermus_filiformis Thermus filiformis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dgt 1dgt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9P OCA].

	==Reference==		==Reference==
-	Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications., Lee JY, Chang C, Song HK, Moon J, Yang JK, Kim HK, Kwon ST, Suh SW, EMBO J. 2000 Mar 1;19(5):1119-29. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/10698952 10698952]~~	+	<ref group="xtra">PMID:10698952</ref><references group="xtra"/>
-	~~[[Category: Single protein]]~~	+
	[[Category: Thermus filiformis]]		[[Category: Thermus filiformis]]
	[[Category: Chang, C.]]		[[Category: Chang, C.]]
Line 36:		Line 35:
	[[Category: Nad+-dependent dna ligase]]		[[Category: Nad+-dependent dna ligase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 02~~:29~~:20 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:30:29 2009''