3jsn - Revision history

OCA at 10:13, 21 February 2024

OCA — Wed, 21 Feb 2024 10:13:11 GMT

←Older revision		Revision as of 10:13, 21 February 2024
Line 1:		Line 1:

	==Crystal structure of the adenylation domain of NAD+-dependent DNA ligase from Staphylococcus aureus==		==Crystal structure of the adenylation domain of NAD+-dependent DNA ligase from Staphylococcus aureus==
-	<StructureSection load='3jsn' size='340' side='right' caption='[[3jsn]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='3jsn' size='340' side='right'caption='[[3jsn]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3jsn]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus~~ aureus~~" (rosenbach 1884) zopf 1885~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JSN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3JSN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3jsn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JSN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JSN FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[3jsl\|3jsl]]</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~~='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=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</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=3jsn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jsn OCA], [https://pdbe.org/3jsn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jsn RCSB], [https://www.ebi.ac.uk/pdbsum/3jsn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jsn 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~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3jsn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jsn OCA], [~~http~~://pdbe.org/3jsn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3jsn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3jsn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3jsn ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DNLJ_STAAU DNLJ_STAAU]
	== 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=3jsn 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=3jsn ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	DNA ligase catalyzes phosphodiester-bond formation between immediately adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA and plays a central role in many cellular and biochemical processes, including DNA replication, repair and recombination. Bacterial NAD(+)-dependent DNA ligases have been extensively characterized as potential antibacterial targets because of their essentiality and their structural distinction from human ATP-dependent DNA ligases. The high-resolution structure of the adenylation domain of Staphylococcus aureus NAD(+)-dependent DNA ligase establishes the conserved domain architecture with other bacterial adenylation domains. Two apo crystal structures revealed that the active site possesses the preformed NAD(+)-binding pocket and the 'C2 tunnel' lined with hydrophobic residues: Leu80, Phe224, Leu287, Phe295 and Trp302. The C2 tunnel is unique to bacterial DNA ligases and the Leu80 side chain at the mouth of the tunnel points inside the tunnel and forms a narrow funnel in the S. aureus DNA ligase structure. Taken together with other DNA ligase structures, the S. aureus DNA ligase structure provides a basis for a more integrated understanding of substrate recognition and catalysis and will be also be of help in the development of small-molecule inhibitors.
-
-	Structure of the adenylation domain of NAD(+)-dependent DNA ligase from Staphylococcus aureus.,Han S, Chang JS, Griffor M Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Nov 1;65(Pt, 11):1078-82. Epub 2009 Oct 13. PMID:19923722<ref>PMID:19923722</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3jsn" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[DNA ligase\|DNA ligase]]	+	*[[DNA ligase 3D structures\|DNA ligase 3D structures]]
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Chang, J S]]~~	+	[[Category: Large Structures]]
-	~~[[Category: Griffor, M]]~~	+
-	~~[[Category: Han, S]]~~	+
-	~~[[Category: Adenylation domain]]~~	+
-	~~[[Category: Dna damage]]~~	+
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Dna replication]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Magnesium]]~~	+
-	~~[[Category: Manganese]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Nad]]~~	+
-	~~[[Category: Nad+-dependent dna ligase~~]]	+
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
-	[[Category: ~~Zinc~~]]	+	[[Category: Chang JS]]
		+	[[Category: Griffor M]]
		+	[[Category: Han S]]

OCA at 09:22, 26 December 2018

OCA — Wed, 26 Dec 2018 09:22:39 GMT

←Older revision		Revision as of 09:22, 26 December 2018
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/js/3jsn_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/js/3jsn_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 49:		Line 49:
	[[Category: Nad+-dependent dna ligase]]		[[Category: Nad+-dependent dna ligase]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
		+	[[Category: Zinc]]

OCA at 16:19, 5 August 2016

OCA — Fri, 05 Aug 2016 16:19:48 GMT

←Older revision		Revision as of 16:19, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the adenylation domain of NAD+-dependent DNA ligase from Staphylococcus aureus==		==Crystal structure of the adenylation domain of NAD+-dependent DNA ligase from Staphylococcus aureus==
	<StructureSection load='3jsn' size='340' side='right' caption='[[3jsn]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3jsn' size='340' side='right' caption='[[3jsn]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3jsn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Staphylococcus_aureus Staphylococcus~~ aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JSN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JSN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3jsn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JSN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JSN FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jsl\|3jsl]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jsl\|3jsl]]</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=1280 ~~Staphylococcus~~ aureus])</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=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</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=3jsn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jsn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3jsn RCSB], [http://www.ebi.ac.uk/pdbsum/3jsn 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=3jsn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jsn OCA], [http://pdbe.org/3jsn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jsn RCSB], [http://www.ebi.ac.uk/pdbsum/3jsn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3jsn ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 17:
	<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=3jsn ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 27:
	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 3jsn" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Staphylococcus aureus]]
	[[Category: Chang, J S]]		[[Category: Chang, J S]]
	[[Category: Griffor, M]]		[[Category: Griffor, M]]
Line 47:		Line 48:
	[[Category: Nad]]		[[Category: Nad]]
	[[Category: Nad+-dependent dna ligase]]		[[Category: Nad+-dependent dna ligase]]
		+	[[Category: Staphylococcus aureus]]

OCA at 20:12, 25 December 2014

OCA — Thu, 25 Dec 2014 20:12:57 GMT

←Older revision		Revision as of 20:12, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3jsn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JSN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JSN FirstGlance]. <br>		<table><tr><td colspan='2'>[[3jsn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JSN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JSN FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jsl\|3jsl]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jsl\|3jsl]]</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=1280 Staphylococcus aureus])</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=1280 Staphylococcus aureus])</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=3jsn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jsn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3jsn RCSB], [http://www.ebi.ac.uk/pdbsum/3jsn 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=3jsn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jsn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3jsn RCSB], [http://www.ebi.ac.uk/pdbsum/3jsn 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 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
-	[[Category: Chang, J S.]]	+	[[Category: Chang, J S]]
-	[[Category: Griffor, M.]]	+	[[Category: Griffor, M]]
-	[[Category: Han, S.]]	+	[[Category: Han, S]]
	[[Category: Adenylation domain]]		[[Category: Adenylation domain]]
	[[Category: Dna damage]]		[[Category: Dna damage]]
Line 47:		Line 47:
	[[Category: Nad]]		[[Category: Nad]]
	[[Category: Nad+-dependent dna ligase]]		[[Category: Nad+-dependent dna ligase]]
-	[[Category: Staphylococcus aureus]]

OCA at 12:27, 29 September 2014

OCA — Mon, 29 Sep 2014 12:27:42 GMT

←Older revision		Revision as of 12:27, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3jsn.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the adenylation domain of NAD+-dependent DNA ligase from Staphylococcus aureus==
		+	<StructureSection load='3jsn' size='340' side='right' caption='[[3jsn]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3jsn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JSN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JSN FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jsl\|3jsl]]</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=1280 Staphylococcus aureus])</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=3jsn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jsn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3jsn RCSB], [http://www.ebi.ac.uk/pdbsum/3jsn 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/js/3jsn_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 catalyzes phosphodiester-bond formation between immediately adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA and plays a central role in many cellular and biochemical processes, including DNA replication, repair and recombination. Bacterial NAD(+)-dependent DNA ligases have been extensively characterized as potential antibacterial targets because of their essentiality and their structural distinction from human ATP-dependent DNA ligases. The high-resolution structure of the adenylation domain of Staphylococcus aureus NAD(+)-dependent DNA ligase establishes the conserved domain architecture with other bacterial adenylation domains. Two apo crystal structures revealed that the active site possesses the preformed NAD(+)-binding pocket and the 'C2 tunnel' lined with hydrophobic residues: Leu80, Phe224, Leu287, Phe295 and Trp302. The C2 tunnel is unique to bacterial DNA ligases and the Leu80 side chain at the mouth of the tunnel points inside the tunnel and forms a narrow funnel in the S. aureus DNA ligase structure. Taken together with other DNA ligase structures, the S. aureus DNA ligase structure provides a basis for a more integrated understanding of substrate recognition and catalysis and will be also be of help in the development of small-molecule inhibitors.

-	~~{{STRUCTURE_3jsn\| PDB=3jsn \| SCENE= }}~~	+	Structure of the adenylation domain of NAD(+)-dependent DNA ligase from Staphylococcus aureus.,Han S, Chang JS, Griffor M Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Nov 1;65(Pt, 11):1078-82. Epub 2009 Oct 13. PMID:19923722<ref>PMID:19923722</ref>

-	~~===Crystal structure~~ of the ~~adenylation domain of NAD+-dependent DNA ligase from Staphylococcus aureus===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19923722}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3jsn]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Staphylococcus_aureus Staphylococcus aureus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3JSN OCA].~~	+

	==See Also==		==See Also==
	*[[DNA ligase\|DNA ligase]]		*[[DNA ligase\|DNA ligase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019923722<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
	[[Category: Chang, J S.]]		[[Category: Chang, J S.]]

OCA at 20:58, 20 October 2012

OCA — Sat, 20 Oct 2012 20:58:44 GMT

←Older revision		Revision as of 20:58, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3jsn]] is a 1 chain structure ~~of [[DNA ligase]]~~ with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JSN OCA].	+	[[3jsn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JSN OCA].

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

OCA: Protected "3jsn" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 12:12:40 GMT

Protected "3jsn" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:12, 27 July 2012

OCA at 12:12, 27 July 2012

OCA — Fri, 27 Jul 2012 12:12:37 GMT

←Older revision		Revision as of 12:12, 27 July 2012
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-	~~{{Seed}}~~	+	[[Image:3jsn.png\|left\|200px]]
-	[[Image:3jsn.~~jpg~~\|left\|200px]]	+

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3jsn", 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_3jsn\| PDB=3jsn \| SCENE= }}		{{STRUCTURE_3jsn\| PDB=3jsn \| SCENE= }}

	===Crystal structure of the adenylation domain of NAD+-dependent DNA ligase from Staphylococcus aureus===		===Crystal structure of the adenylation domain of NAD+-dependent DNA ligase from Staphylococcus aureus===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19923722}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19923722 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19923722}}		{{ABSTRACT_PUBMED_19923722}}

	==About this Structure==		==About this Structure==
-	~~3JSN~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JSN OCA].	+	[[3jsn]] is a 1 chain structure of [[DNA ligase]] with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JSN OCA].
		+
		+	==See Also==
		+	*[[DNA ligase\|DNA ligase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19923722~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019923722</ref><references group="xtra"/>
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
	[[Category: Chang, J S.]]		[[Category: Chang, J S.]]
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	[[Category: Nad+-dependent dna ligase]]		[[Category: Nad+-dependent dna ligase]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
-	[[Category: Zinc]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 16 13:03:00 2009''

OCA at 11:03, 16 December 2009

OCA — Wed, 16 Dec 2009 11:03:02 GMT

←Older revision		Revision as of 11:03, 16 December 2009
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3jsn.jpg\|left\|200px]]

-	The ~~entry 3jsn~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3jsn", 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_3jsn\| PDB=3jsn \| SCENE= }}

-	~~Authors: Han, S., Chang, J.S., Griffor, M.~~	+	===Crystal structure of the adenylation domain of NAD+-dependent DNA ligase from Staphylococcus aureus===

-	Description: Crystal structure of the adenylation domain of NAD+-dependent DNA ligase from Staphylococcus aureus

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Oct 21 09~~:59:44 2009''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19923722}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19923722 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19923722}}
		+
		+	==About this Structure==
		+	3JSN is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JSN OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19923722</ref><references group="xtra"/>
		+	[[Category: Staphylococcus aureus]]
		+	[[Category: Chang, J S.]]
		+	[[Category: Griffor, M.]]
		+	[[Category: Han, S.]]
		+	[[Category: Adenylation domain]]
		+	[[Category: Dna damage]]
		+	[[Category: Dna repair]]
		+	[[Category: Dna replication]]
		+	[[Category: Ligase]]
		+	[[Category: Magnesium]]
		+	[[Category: Manganese]]
		+	[[Category: Metal-binding]]
		+	[[Category: Nad]]
		+	[[Category: Nad+-dependent dna ligase]]
		+	[[Category: Staphylococcus aureus]]
		+	[[Category: Zinc]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 16 13:03:00 2009''

OCA at 07:59, 21 October 2009

OCA — Wed, 21 Oct 2009 07:59:44 GMT

←Older revision		Revision as of 07:59, 21 October 2009
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3jsn is ON HOLD	+	The entry 3jsn is ON HOLD until Paper Publication

	Authors: Han, S., Chang, J.S., Griffor, M.		Authors: Han, S., Chang, J.S., Griffor, M.
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	Description: Crystal structure of the adenylation domain of NAD+-dependent DNA ligase from Staphylococcus aureus		Description: Crystal structure of the adenylation domain of NAD+-dependent DNA ligase from Staphylococcus aureus

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Sep 23 08~~:30:29 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 21 09:59:44 2009''