3sng - Revision history

OCA at 13:02, 14 March 2024

OCA — Thu, 14 Mar 2024 13:02:29 GMT

←Older revision		Revision as of 13:02, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3sng' size='340' side='right'caption='[[3sng]], [[Resolution\|resolution]] 2.16Å' scene=''>		<StructureSection load='3sng' size='340' side='right'caption='[[3sng]], [[Resolution\|resolution]] 2.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3sng]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Lycopersicon_esculentum Lycopersicon esculentum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SNG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SNG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3sng]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SNG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SNG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=~~SO4~~:~~SULFATE+ION~~'>~~SO4~~</scene>, <scene name='pdbligand=ZN:~~ZINC+ION~~'>ZN</scene>, <scene name='pdbligand=~~MAN~~:~~ALPHA-D-MANNOSE~~'>~~MAN~~</scene>, <scene name='pdbligand=~~NAG~~:~~N-ACETYL-D-GLUCOSAMINE~~'>~~NAG~~</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]] 2.16Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tbn1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4081 Lycopersicon esculentum])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=3sng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sng OCA], [https://pdbe.org/3sng PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sng RCSB], [https://www.ebi.ac.uk/pdbsum/3sng PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sng 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=3sng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sng OCA], [https://pdbe.org/3sng PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sng RCSB], [https://www.ebi.ac.uk/pdbsum/3sng PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sng ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q0KFV0_SOLLC Q0KFV0_SOLLC]
-	Type I plant nucleases play an important role in apoptotic processes and cell senescence. Recently, they have also been indicated to be potent anticancer agents in in vivo studies. The first structure of tomato nuclease I (TBN1) has been determined, its oligomerization and activity profiles have been analyzed and its unexpected activity towards phospholipids has been discovered, and conclusions are drawn regarding its catalytic mechanism. The structure-solution process required X-ray diffraction data from two crystal forms. The first form was used for phase determination; the second form was used for model building and refinement. TBN1 is mainly alpha-helical and is stabilized by four disulfide bridges. Three observed oligosaccharides are crucial for its stability and solubility. The active site is localized at the bottom of the positively charged groove and contains a zinc cluster that is essential for enzymatic activity. An equilibrium between monomers, dimers and higher oligomers of TBN1 was observed in solution. Principles of the reaction mechanism of the phosphodiesterase activity are suggested, with central roles for the zinc cluster, the nucleobase-binding pocket (Phe-site) and Asp70, Arg73 and Asn167. Based on the distribution of surface residues, possible binding sites for dsDNA and other nucleic acids with secondary structure were identified. The phospholipase activity of TBN1, which is reported for the first time for a nuclease, significantly broadens the substrate promiscuity of the enzyme, and the resulting release of diacylglycerol, which is an important second messenger, can be related to the role of TBN1 in apoptosis.	+
-		+
-	~~Plant multifunctional nuclease TBN1 with unexpected phospholipase activity~~: structural study and reaction-mechanism analysis.,Koval' T, Lipovova P, Podzimek T, Matousek J, Duskova J, Skalova T, Stepankova A, Hasek J, Dohnalek J Acta Crystallogr D Biol Crystallogr. 2013 Feb;69(Pt 2):213-26. doi:, 10.1107/~~S0907444912043697. Epub 2013 Jan 16. PMID:23385457<ref>PMID:23385457<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 3sng" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lycopersicon esculentum~~]]	+	[[Category: Solanum lycopersicum]]
-	[[Category: Dohnalek, J]]	+	[[Category: Dohnalek J]]
-	[[Category: Duskova, J]]	+	[[Category: Duskova J]]
-	[[Category: Hasek, J]]	+	[[Category: Hasek J]]
-	[[Category: Koval, T]]	+	[[Category: Koval T]]
-	[[Category: Lipovova, P]]	+	[[Category: Lipovova P]]
-	[[Category: Matousek, J]]	+	[[Category: Matousek J]]
-	[[Category: Podzimek, T]]	+	[[Category: Podzimek T]]
-	[[Category: Skalova, T]]	+	[[Category: Skalova T]]
-	[[Category: Stepankova, A]]	+	[[Category: Stepankova A]]
-	~~[[Category: 3'-nucleotidase]]~~	+
-	~~[[Category: Bi-functional]]~~	+
-	~~[[Category: Cytosol membrane associated]]~~	+
-	~~[[Category: Endonuclease]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Mainly alpha helical]]~~	+
-	~~[[Category: Mononucleotide]]~~	+
-	~~[[Category: Nucleic acid]]~~	+
-	~~[[Category: Trinuclear metal centre~~]]	+

OCA at 08:02, 29 June 2022

OCA — Wed, 29 Jun 2022 08:02:59 GMT

←Older revision		Revision as of 08:02, 29 June 2022
Line 1:		Line 1:

	==X-ray structure of fully glycosylated bifunctional nuclease TBN1 from Solanum lycopersicum (Tomato)==		==X-ray structure of fully glycosylated bifunctional nuclease TBN1 from Solanum lycopersicum (Tomato)==
-	<StructureSection load='3sng' size='340' side='right' caption='[[3sng]], [[Resolution\|resolution]] 2.16Å' scene=''>	+	<StructureSection load='3sng' size='340' side='right'caption='[[3sng]], [[Resolution\|resolution]] 2.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3sng]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Lycopersicon_esculentum Lycopersicon esculentum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SNG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3SNG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3sng]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lycopersicon_esculentum Lycopersicon esculentum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SNG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SNG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=~~MAN~~:~~ALPHA-D-MANNOSE~~'>~~MAN~~</scene>, <scene name='pdbligand=~~NAG~~:~~N-ACETYL-D-GLUCOSAMINE~~'>~~NAG~~</scene>, <scene name='pdbligand=~~SO4~~:~~SULFATE+ION~~'>~~SO4~~</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=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tbn1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4081 Lycopersicon esculentum])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tbn1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4081 Lycopersicon esculentum])</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=3sng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sng OCA], [~~http~~://pdbe.org/3sng PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3sng RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3sng PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3sng 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=3sng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sng OCA], [https://pdbe.org/3sng PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sng RCSB], [https://www.ebi.ac.uk/pdbsum/3sng PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sng ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lycopersicon esculentum]]		[[Category: Lycopersicon esculentum]]
	[[Category: Dohnalek, J]]		[[Category: Dohnalek, J]]

OCA at 09:39, 8 November 2017

OCA — Wed, 08 Nov 2017 09:39:49 GMT

←Older revision		Revision as of 09:39, 8 November 2017
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3sng]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lycopersicon_esculentum Lycopersicon esculentum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SNG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SNG FirstGlance]. <br>		<table><tr><td colspan='2'>[[3sng]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lycopersicon_esculentum Lycopersicon esculentum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SNG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SNG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=~~SO4~~:~~SULFATE+ION~~'>~~SO4~~</scene>, <scene name='pdbligand=ZN:~~ZINC+ION~~'>ZN</scene>, <scene name='pdbligand=~~MAN~~:~~ALPHA-D-MANNOSE~~'>~~MAN~~</scene>, <scene name='pdbligand=~~NAG~~:~~N-ACETYL-D-GLUCOSAMINE~~'>~~NAG~~</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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">tbn1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4081 Lycopersicon esculentum])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tbn1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4081 Lycopersicon esculentum])</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=3sng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sng OCA], [http://pdbe.org/3sng PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3sng RCSB], [http://www.ebi.ac.uk/pdbsum/3sng PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3sng ProSAT]</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=3sng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sng OCA], [http://pdbe.org/3sng PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3sng RCSB], [http://www.ebi.ac.uk/pdbsum/3sng PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3sng ProSAT]</span></td></tr>

OCA at 19:40, 11 August 2016

OCA — Thu, 11 Aug 2016 19:40:54 GMT

←Older revision		Revision as of 19:40, 11 August 2016
Line 1:		Line 1:
		+
	==X-ray structure of fully glycosylated bifunctional nuclease TBN1 from Solanum lycopersicum (Tomato)==		==X-ray structure of fully glycosylated bifunctional nuclease TBN1 from Solanum lycopersicum (Tomato)==
	<StructureSection load='3sng' size='340' side='right' caption='[[3sng]], [[Resolution\|resolution]] 2.16Å' scene=''>		<StructureSection load='3sng' size='340' side='right' caption='[[3sng]], [[Resolution\|resolution]] 2.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3sng]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Solanum_lycopersicum Solanum lycopersicum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SNG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SNG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3sng]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lycopersicon_esculentum Lycopersicon esculentum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SNG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SNG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tbn1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4081 ~~Solanum lycopersicum~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tbn1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4081 Lycopersicon esculentum])</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=3sng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sng OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3sng RCSB], [http://www.ebi.ac.uk/pdbsum/3sng 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=3sng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sng OCA], [http://pdbe.org/3sng PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3sng RCSB], [http://www.ebi.ac.uk/pdbsum/3sng PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3sng ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 3sng" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Solanum lycopersicum~~]]	+	[[Category: Lycopersicon esculentum]]
	[[Category: Dohnalek, J]]		[[Category: Dohnalek, J]]
	[[Category: Duskova, J]]		[[Category: Duskova, J]]

OCA at 09:19, 4 January 2015

OCA — Sun, 04 Jan 2015 09:19:03 GMT

←Older revision		Revision as of 09:19, 4 January 2015
Line 1:		Line 1:
-	[[~~Image:~~3sng.~~png~~\|~~left~~\|~~200px~~]]	+	==X-ray structure of fully glycosylated bifunctional nuclease TBN1 from Solanum lycopersicum (Tomato)==
		+	<StructureSection load='3sng' size='340' side='right' caption='[[3sng]], [[Resolution\|resolution]] 2.16Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3sng]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SNG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SNG FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tbn1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4081 Solanum lycopersicum])</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=3sng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sng OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3sng RCSB], [http://www.ebi.ac.uk/pdbsum/3sng PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Type I plant nucleases play an important role in apoptotic processes and cell senescence. Recently, they have also been indicated to be potent anticancer agents in in vivo studies. The first structure of tomato nuclease I (TBN1) has been determined, its oligomerization and activity profiles have been analyzed and its unexpected activity towards phospholipids has been discovered, and conclusions are drawn regarding its catalytic mechanism. The structure-solution process required X-ray diffraction data from two crystal forms. The first form was used for phase determination; the second form was used for model building and refinement. TBN1 is mainly alpha-helical and is stabilized by four disulfide bridges. Three observed oligosaccharides are crucial for its stability and solubility. The active site is localized at the bottom of the positively charged groove and contains a zinc cluster that is essential for enzymatic activity. An equilibrium between monomers, dimers and higher oligomers of TBN1 was observed in solution. Principles of the reaction mechanism of the phosphodiesterase activity are suggested, with central roles for the zinc cluster, the nucleobase-binding pocket (Phe-site) and Asp70, Arg73 and Asn167. Based on the distribution of surface residues, possible binding sites for dsDNA and other nucleic acids with secondary structure were identified. The phospholipase activity of TBN1, which is reported for the first time for a nuclease, significantly broadens the substrate promiscuity of the enzyme, and the resulting release of diacylglycerol, which is an important second messenger, can be related to the role of TBN1 in apoptosis.

-	~~{{STRUCTURE_3sng\| PDB=3sng \| SCENE= }}~~	+	Plant multifunctional nuclease TBN1 with unexpected phospholipase activity: structural study and reaction-mechanism analysis.,Koval' T, Lipovova P, Podzimek T, Matousek J, Duskova J, Skalova T, Stepankova A, Hasek J, Dohnalek J Acta Crystallogr D Biol Crystallogr. 2013 Feb;69(Pt 2):213-26. doi:, 10.1107/S0907444912043697. Epub 2013 Jan 16. PMID:23385457<ref>PMID:23385457</ref>

-	~~===X-ray structure~~ of ~~fully glycosylated bifunctional nuclease TBN1 from Solanum lycopersicum (Tomato)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_23385457}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[3sng]] is a 1 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SNG OCA].~~	+	</StructureSection>
	[[Category: Solanum lycopersicum]]		[[Category: Solanum lycopersicum]]
-	[[Category: Dohnalek, J.]]	+	[[Category: Dohnalek, J]]
-	[[Category: Duskova, J.]]	+	[[Category: Duskova, J]]
-	[[Category: Hasek, J.]]	+	[[Category: Hasek, J]]
-	[[Category: Koval, T.]]	+	[[Category: Koval, T]]
-	[[Category: Lipovova, P.]]	+	[[Category: Lipovova, P]]
-	[[Category: Matousek, J.]]	+	[[Category: Matousek, J]]
-	[[Category: Podzimek, T.]]	+	[[Category: Podzimek, T]]
-	[[Category: Skalova, T.]]	+	[[Category: Skalova, T]]
-	[[Category: Stepankova, A.]]	+	[[Category: Stepankova, A]]
	[[Category: 3'-nucleotidase]]		[[Category: 3'-nucleotidase]]
	[[Category: Bi-functional]]		[[Category: Bi-functional]]

OCA at 12:55, 20 February 2013

OCA — Wed, 20 Feb 2013 12:55:22 GMT

←Older revision		Revision as of 12:55, 20 February 2013
Line 5:		Line 5:
	===X-ray structure of fully glycosylated bifunctional nuclease TBN1 from Solanum lycopersicum (Tomato)===		===X-ray structure of fully glycosylated bifunctional nuclease TBN1 from Solanum lycopersicum (Tomato)===

		+	{{ABSTRACT_PUBMED_23385457}}

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

OCA at 12:47, 30 January 2013

OCA — Wed, 30 Jan 2013 12:47:51 GMT

←Older revision		Revision as of 12:47, 30 January 2013
Line 1:		Line 1:
-	[[Image:3sng.~~jpg~~\|left\|200px]]	+	[[Image:3sng.png\|left\|200px]]

	{{STRUCTURE_3sng\| PDB=3sng \| SCENE= }}		{{STRUCTURE_3sng\| PDB=3sng \| SCENE= }}

OCA at 07:42, 4 July 2012

OCA — Wed, 04 Jul 2012 07:42:56 GMT

←Older revision		Revision as of 07:42, 4 July 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3sng.jpg\|left\|200px]]

-	~~The entry~~ 3sng ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_3sng\| PDB=3sng \| SCENE= }}

-	~~Authors: Koval, T., Stepankova, A., Lipovova, P., Podzimek, T., Matousek, J., Duskova, J., Skalova, T., Hasek, J., Dohnalek, J.~~	+	===X-ray structure of fully glycosylated bifunctional nuclease TBN1 from Solanum lycopersicum (Tomato)===

-	~~Description: X-ray~~ structure ~~of fully glycosylated bifunctional nuclease TBN1~~ from Solanum lycopersicum ~~(Tomato)~~	+
		+	==About this Structure==
		+	[[3sng]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SNG OCA].
		+	[[Category: Solanum lycopersicum]]
		+	[[Category: Dohnalek, J.]]
		+	[[Category: Duskova, J.]]
		+	[[Category: Hasek, J.]]
		+	[[Category: Koval, T.]]
		+	[[Category: Lipovova, P.]]
		+	[[Category: Matousek, J.]]
		+	[[Category: Podzimek, T.]]
		+	[[Category: Skalova, T.]]
		+	[[Category: Stepankova, A.]]
		+	[[Category: 3'-nucleotidase]]
		+	[[Category: Bi-functional]]
		+	[[Category: Cytosol membrane associated]]
		+	[[Category: Endonuclease]]
		+	[[Category: Hydrolase]]
		+	[[Category: Mainly alpha helical]]
		+	[[Category: Mononucleotide]]
		+	[[Category: Nucleic acid]]
		+	[[Category: Trinuclear metal centre]]

OCA at 08:20, 3 August 2011

OCA — Wed, 03 Aug 2011 08:20:12 GMT

←Older revision		Revision as of 08:20, 3 August 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Koval, T., Stepankova, A., Lipovova, P., Podzimek, T., Matousek, J., Duskova, J., Skalova, T., Hasek, J., Dohnalek, J.		Authors: Koval, T., Stepankova, A., Lipovova, P., Podzimek, T., Matousek, J., Duskova, J., Skalova, T., Hasek, J., Dohnalek, J.

	Description: X-ray structure of fully glycosylated bifunctional nuclease TBN1 from Solanum lycopersicum (Tomato)		Description: X-ray structure of fully glycosylated bifunctional nuclease TBN1 from Solanum lycopersicum (Tomato)

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

OCA — Wed, 06 Jul 2011 18:29:50 GMT

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

←Older revision

Revision as of 18:29, 6 July 2011