3ty5 - Revision history

OCA at 10:15, 1 March 2024

OCA — Fri, 01 Mar 2024 10:15:46 GMT

←Older revision		Revision as of 10:15, 1 March 2024
Line 3:		Line 3:
	<StructureSection load='3ty5' size='340' side='right'caption='[[3ty5]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3ty5' size='340' side='right'caption='[[3ty5]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ty5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Acet2 Acet2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TY5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TY5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ty5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetivibrio_thermocellus_ATCC_27405 Acetivibrio thermocellus ATCC 27405]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TY5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TY5 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ADP:ADENOSINE~~-~~5-DIPHOSPHATE'>ADP</scene>~~, ~~<scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 2.4Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Cthe_2768 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id=203119 ACET2])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/RNA_ligase_(ATP) RNA ligase (ATP)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.3 6.5.1.3]~~ </~~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=3ty5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ty5 OCA], [https://pdbe.org/3ty5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ty5 RCSB], [https://www.ebi.ac.uk/pdbsum/3ty5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ty5 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=3ty5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ty5 OCA], [https://pdbe.org/3ty5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ty5 RCSB], [https://www.ebi.ac.uk/pdbsum/3ty5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ty5 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A3DJ38_ACET2 A3DJ38_ACET2]
-	Pnkp is the end-healing and end-sealing component of an RNA repair system present in diverse bacteria from ten different phyla. To gain insight to the mechanism and evolution of this repair system, we determined the crystal structures of the ligase domain of Clostridium thermocellum Pnkp in three functional states along the reaction pathway: apoenzyme, ligase*ATP substrate complex, and covalent ligase-AMP intermediate. The tertiary structure is composed of a classical ligase nucleotidyltransferase module that is embellished by a unique alpha-helical insert module and a unique C-terminal alpha-helical module. Structure-guided mutational analysis identified active site residues essential for ligase adenylylation. Pnkp defines a new RNA ligase family with signature structural and functional properties.	+
-		+
-	The adenylyltransferase domain of bacterial Pnkp defines a unique RNA ligase family.,Smith P, Wang LK, Nair PA, Shuman S Proc Natl Acad Sci U S A. 2012 Feb 14;109(7):2296-301. Epub 2012 Jan 27. PMID:22308407<ref>PMID:22308407</~~ref>~~	+
-		+
-	~~From MEDLINE®~~/~~PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 3ty5" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Acet2~~]]	+	[[Category: Acetivibrio thermocellus ATCC 27405]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Shuman, S]]	+	[[Category: Shuman S]]
-	[[Category: Smith, P]]	+	[[Category: Smith P]]
-	[[Category: Wang, L]]	+	[[Category: Wang L]]
-	~~[[Category: Adenylyltransferase]]~~	+
-	~~[[Category: Dna ligase/mrna capping enzyme]]~~	+
-	~~[[Category: Hen1]]~~	+
-	~~[[Category: Rna ligase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 05:50, 13 July 2022

OCA — Wed, 13 Jul 2022 05:50:04 GMT

←Older revision		Revision as of 05:50, 13 July 2022
Line 1:		Line 1:

	==Crystal Structure of C. thermocellum PNKP Ligase domain in complex with ATP==		==Crystal Structure of C. thermocellum PNKP Ligase domain in complex with ATP==
-	<StructureSection load='3ty5' size='340' side='right' caption='[[3ty5]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='3ty5' size='340' side='right'caption='[[3ty5]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ty5]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Cloth Cloth~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TY5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3TY5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ty5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acet2 Acet2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TY5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TY5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cthe_2768 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=203119 ~~CLOTH~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cthe_2768 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=203119 ACET2])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/RNA_ligase_(ATP) RNA ligase (ATP)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.3 6.5.1.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/RNA_ligase_(ATP) RNA ligase (ATP)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.3 6.5.1.3] </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=3ty5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ty5 OCA], [~~http~~://pdbe.org/3ty5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ty5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ty5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ty5 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=3ty5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ty5 OCA], [https://pdbe.org/3ty5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ty5 RCSB], [https://www.ebi.ac.uk/pdbsum/3ty5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ty5 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cloth~~]]	+	[[Category: Acet2]]
		+	[[Category: Large Structures]]
	[[Category: Shuman, S]]		[[Category: Shuman, S]]
	[[Category: Smith, P]]		[[Category: Smith, P]]

OCA at 17:23, 11 August 2016

OCA — Thu, 11 Aug 2016 17:23:43 GMT

←Older revision		Revision as of 17:23, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of C. thermocellum PNKP Ligase domain in complex with ATP==		==Crystal Structure of C. thermocellum PNKP Ligase domain in complex with ATP==
	<StructureSection load='3ty5' size='340' side='right' caption='[[3ty5]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3ty5' size='340' side='right' caption='[[3ty5]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ty5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Clostridium_thermocellum Clostridium thermocellum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TY5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TY5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ty5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cloth Cloth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TY5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TY5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cthe_2768 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~1515 Clostridium thermocellum~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cthe_2768 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=203119 CLOTH])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_ligase_(ATP) RNA ligase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.3 6.5.1.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_ligase_(ATP) RNA ligase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.3 6.5.1.3] </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=3ty5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ty5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ty5 RCSB], [http://www.ebi.ac.uk/pdbsum/3ty5 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=3ty5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ty5 OCA], [http://pdbe.org/3ty5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ty5 RCSB], [http://www.ebi.ac.uk/pdbsum/3ty5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ty5 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 3ty5" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Clostridium thermocellum~~]]	+	[[Category: Cloth]]
	[[Category: Shuman, S]]		[[Category: Shuman, S]]
	[[Category: Smith, P]]		[[Category: Smith, P]]

OCA at 10:54, 4 January 2015

OCA — Sun, 04 Jan 2015 10:54:02 GMT

←Older revision		Revision as of 10:54, 4 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ty5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_thermocellum Clostridium thermocellum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TY5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TY5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ty5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_thermocellum Clostridium thermocellum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TY5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TY5 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cthe_2768 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1515 Clostridium thermocellum])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cthe_2768 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1515 Clostridium thermocellum])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_ligase_(ATP) RNA ligase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.3 6.5.1.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_ligase_(ATP) RNA ligase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.3 6.5.1.3] </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=3ty5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ty5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ty5 RCSB], [http://www.ebi.ac.uk/pdbsum/3ty5 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=3ty5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ty5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ty5 RCSB], [http://www.ebi.ac.uk/pdbsum/3ty5 PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 14:		Line 14:
	The adenylyltransferase domain of bacterial Pnkp defines a unique RNA ligase family.,Smith P, Wang LK, Nair PA, Shuman S Proc Natl Acad Sci U S A. 2012 Feb 14;109(7):2296-301. Epub 2012 Jan 27. PMID:22308407<ref>PMID:22308407</ref>		The adenylyltransferase domain of bacterial Pnkp defines a unique RNA ligase family.,Smith P, Wang LK, Nair PA, Shuman S Proc Natl Acad Sci U S A. 2012 Feb 14;109(7):2296-301. Epub 2012 Jan 27. PMID:22308407<ref>PMID:22308407</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Clostridium thermocellum]]		[[Category: Clostridium thermocellum]]
-	[[Category: Shuman, S.]]	+	[[Category: Shuman, S]]
-	[[Category: Smith, P.]]	+	[[Category: Smith, P]]
-	[[Category: Wang, L.]]	+	[[Category: Wang, L]]
	[[Category: Adenylyltransferase]]		[[Category: Adenylyltransferase]]
	[[Category: Dna ligase/mrna capping enzyme]]		[[Category: Dna ligase/mrna capping enzyme]]

OCA at 06:32, 5 June 2014

OCA — Thu, 05 Jun 2014 06:32:00 GMT

←Older revision		Revision as of 06:32, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3ty5.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal Structure of C. thermocellum PNKP Ligase domain in complex with ATP==
		+	<StructureSection load='3ty5' size='340' side='right' caption='[[3ty5]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ty5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_thermocellum Clostridium thermocellum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TY5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TY5 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cthe_2768 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1515 Clostridium thermocellum])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_ligase_(ATP) RNA ligase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.3 6.5.1.3] </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=3ty5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ty5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ty5 RCSB], [http://www.ebi.ac.uk/pdbsum/3ty5 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pnkp is the end-healing and end-sealing component of an RNA repair system present in diverse bacteria from ten different phyla. To gain insight to the mechanism and evolution of this repair system, we determined the crystal structures of the ligase domain of Clostridium thermocellum Pnkp in three functional states along the reaction pathway: apoenzyme, ligase*ATP substrate complex, and covalent ligase-AMP intermediate. The tertiary structure is composed of a classical ligase nucleotidyltransferase module that is embellished by a unique alpha-helical insert module and a unique C-terminal alpha-helical module. Structure-guided mutational analysis identified active site residues essential for ligase adenylylation. Pnkp defines a new RNA ligase family with signature structural and functional properties.

-	~~<!--~~	+	The adenylyltransferase domain of bacterial Pnkp defines a unique RNA ligase family.,Smith P, Wang LK, Nair PA, Shuman S Proc Natl Acad Sci U S A. 2012 Feb 14;109(7):2296-301. Epub 2012 Jan 27. PMID:22308407<ref>PMID:22308407</ref>
-	The ~~line below this paragraph~~, ~~containing "STRUCTURE_3ty5"~~, ~~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_3ty5\| PDB=3ty5 \| SCENE= }}~~	+

-	~~===Crystal Structure~~ of ~~C. thermocellum PNKP Ligase domain in complex with ATP===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_22308407}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22308407 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_22308407}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3ty5]] is a 2 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Clostridium_thermocellum Clostridium thermocellum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TY5 OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022308407<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Clostridium thermocellum]]		[[Category: Clostridium thermocellum]]
	[[Category: Shuman, S.]]		[[Category: Shuman, S.]]

OCA at 07:41, 29 February 2012

OCA — Wed, 29 Feb 2012 07:41:13 GMT

←Older revision		Revision as of 07:41, 29 February 2012
Line 11:		Line 11:
	===Crystal Structure of C. thermocellum PNKP Ligase domain in complex with ATP===		===Crystal Structure of C. thermocellum PNKP Ligase domain in complex with ATP===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22308407}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22308407 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22308407}}

	==About this Structure==		==About this Structure==

OCA at 06:50, 22 February 2012

OCA — Wed, 22 Feb 2012 06:50:09 GMT

←Older revision		Revision as of 06:50, 22 February 2012
Line 14:		Line 14:
	==About this Structure==		==About this Structure==
	[[3ty5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_thermocellum Clostridium thermocellum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TY5 OCA].		[[3ty5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_thermocellum Clostridium thermocellum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TY5 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022308407</ref><references group="xtra"/>
	[[Category: Clostridium thermocellum]]		[[Category: Clostridium thermocellum]]
	[[Category: Shuman, S.]]		[[Category: Shuman, S.]]

OCA at 07:29, 1 February 2012

OCA — Wed, 01 Feb 2012 07:29:26 GMT

←Older revision		Revision as of 07:29, 1 February 2012
Line 1:		Line 1:
-	[[Image:3ty5.~~jpg~~\|left\|200px]]	+	[[Image:3ty5.png\|left\|200px]]

	<!--		<!--

OCA at 06:45, 25 January 2012

OCA — Wed, 25 Jan 2012 06:45:27 GMT

←Older revision		Revision as of 06:45, 25 January 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3ty5.jpg\|left\|200px]]

-	The ~~entry 3ty5~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3ty5", 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_3ty5\| PDB=3ty5 \| SCENE= }}

-	~~Authors: Smith, P., Wang, L., Shuman, S~~.	+	===Crystal Structure of C. thermocellum PNKP Ligase domain in complex with ATP===

-	~~Description: Crystal~~ Structure ~~of C~~. thermocellum ~~PNKP Ligase domain in complex with ATP~~	+
		+	==About this Structure==
		+	[[3ty5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_thermocellum Clostridium thermocellum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TY5 OCA].
		+	[[Category: Clostridium thermocellum]]
		+	[[Category: Shuman, S.]]
		+	[[Category: Smith, P.]]
		+	[[Category: Wang, L.]]
		+	[[Category: Adenylyltransferase]]
		+	[[Category: Dna ligase/mrna capping enzyme]]
		+	[[Category: Hen1]]
		+	[[Category: Rna ligase]]
		+	[[Category: Transferase]]

OCA at 08:45, 30 October 2011

OCA — Sun, 30 Oct 2011 08:45:52 GMT

←Older revision		Revision as of 08:45, 30 October 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3ty5 is ON HOLD	+	The entry 3ty5 is ON HOLD until Paper Publication

-	Authors: Smith, P, Wang, L, Shuman, S	+	Authors: Smith, P., Wang, L., Shuman, S.

	Description: Crystal Structure of C. thermocellum PNKP Ligase domain in complex with ATP		Description: Crystal Structure of C. thermocellum PNKP Ligase domain in complex with ATP