1lwt - Revision history

OCA at 08:28, 10 April 2024

OCA — Wed, 10 Apr 2024 08:28:43 GMT

←Older revision		Revision as of 08:28, 10 April 2024
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	<StructureSection load='1lwt' size='340' side='right'caption='[[1lwt]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='1lwt' size='340' side='right'caption='[[1lwt]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lwt]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LWT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1LWT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lwt]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LWT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LWT FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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]] 3.2Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[1vde\|1vde]]~~, [[~~1lws~~\|~~1lws~~]]~~</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~VMA1 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])~~</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=1lwt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lwt OCA], [https://pdbe.org/1lwt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lwt RCSB], [https://www.ebi.ac.uk/pdbsum/1lwt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lwt 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=1lwt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lwt OCA], [~~http~~://pdbe.org/1lwt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1lwt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1lwt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1lwt ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/VATA_YEAST VATA_YEAST]] Catalytic subunit of the peripheral V1 complex of vacuolar ATPase. V-ATPase (vacuolar ATPase) is responsible for acidifying a variety of intracellular compartments in eukaryotic cells. It is an electrogenic proton pump that generates a proton motive force of 180 mV, inside positive and acidic, in the vacuolar membrane vesicles. It may participate in maintenance of cytoplasmic Ca(2+) homeostasis. This is a catalytic subunit.<ref>PMID:1534148</ref> PI-SceI is an endonuclease that can cleave at a site present in a VMA1 allele that lacks the derived endonuclease segment of the open reading frame; cleavage at this site only occurs during meiosis and initiates "homing", a genetic event that converts a VMA1 allele lacking VDE into one that contains it.<ref>PMID:1534148</ref>	+	[https://www.uniprot.org/uniprot/VATA_YEAST VATA_YEAST] Catalytic subunit of the peripheral V1 complex of vacuolar ATPase. V-ATPase (vacuolar ATPase) is responsible for acidifying a variety of intracellular compartments in eukaryotic cells. It is an electrogenic proton pump that generates a proton motive force of 180 mV, inside positive and acidic, in the vacuolar membrane vesicles. It may participate in maintenance of cytoplasmic Ca(2+) homeostasis. This is a catalytic subunit.<ref>PMID:1534148</ref> PI-SceI is an endonuclease that can cleave at a site present in a VMA1 allele that lacks the derived endonuclease segment of the open reading frame; cleavage at this site only occurs during meiosis and initiates "homing", a genetic event that converts a VMA1 allele lacking VDE into one that contains it.<ref>PMID:1534148</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1lwt 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=1lwt ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The first X-ray structures of an intein-DNA complex, that of the two-domain homing endonuclease PI-SceI bound to its 36-base pair DNA substrate, have been determined in the presence and absence of Ca(2+). The DNA shows an asymmetric bending pattern, with a major 50 degree bend in the endonuclease domain and a minor 22 degree bend in the splicing domain region. Distortions of the DNA bound to the endonuclease domain cause the insertion of the two cleavage sites in the catalytic center. DNA binding induces changes in the protein conformation. The two overlapping non-identical active sites in the endonucleolytic center contain two Ca(+2) ions that coordinate to the catalytic Asp residues. Structure analysis indicates that the top strand may be cleaved first.
-
-	Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence.,Moure CM, Gimble FS, Quiocho FA Nat Struct Biol. 2002 Oct;9(10):764-70. PMID:12219083<ref>PMID:12219083</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1lwt" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Gimble, F S~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: ~~Moure, C M~~]]	+	[[Category: Gimble FS]]
-	[[Category: ~~Quiocho, F A~~]]	+	[[Category: Moure CM]]
-	[[Category: ~~Endonuclease]]~~	+	[[Category: Quiocho FA]]
-	~~[[Category: Homing endonuclease]]~~	+
-	~~[[Category: Hydrolase-dna complex]]~~	+
-	~~[[Category: Intein]]~~	+
-	~~[[Category: Protein-dna complex~~]]	+

OCA at 08:03, 25 November 2020

OCA — Wed, 25 Nov 2020 08:03:13 GMT

←Older revision		Revision as of 08:03, 25 November 2020
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	==Crystal structure of the intein homing endonuclease PI-SceI bound to its substrate DNA (Ca2+ free)==		==Crystal structure of the intein homing endonuclease PI-SceI bound to its substrate DNA (Ca2+ free)==
-	<StructureSection load='1lwt' size='340' side='right' caption='[[1lwt]], [[Resolution\|resolution]] 3.20Å' scene=''>	+	<StructureSection load='1lwt' size='340' side='right'caption='[[1lwt]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lwt]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LWT OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1LWT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lwt]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LWT OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1LWT FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vde\|1vde]], [[1lws\|1lws]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1vde\|1vde]], [[1lws\|1lws]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VMA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VMA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=1lwt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lwt OCA], [http://pdbe.org/1lwt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lwt RCSB], [http://www.ebi.ac.uk/pdbsum/1lwt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lwt 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=1lwt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lwt OCA], [http://pdbe.org/1lwt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lwt RCSB], [http://www.ebi.ac.uk/pdbsum/1lwt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lwt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lw/1lwt_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lw/1lwt_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 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1lwt" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1lwt" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
		+	[[Category: Large Structures]]
	[[Category: Gimble, F S]]		[[Category: Gimble, F S]]
	[[Category: Moure, C M]]		[[Category: Moure, C M]]

OCA at 10:37, 18 October 2017

OCA — Wed, 18 Oct 2017 10:37:23 GMT

←Older revision		Revision as of 10:37, 18 October 2017
Line 1:		Line 1:
		+
	==Crystal structure of the intein homing endonuclease PI-SceI bound to its substrate DNA (Ca2+ free)==		==Crystal structure of the intein homing endonuclease PI-SceI bound to its substrate DNA (Ca2+ free)==
	<StructureSection load='1lwt' size='340' side='right' caption='[[1lwt]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='1lwt' size='340' side='right' caption='[[1lwt]], [[Resolution\|resolution]] 3.20Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vde\|1vde]], [[1lws\|1lws]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vde\|1vde]], [[1lws\|1lws]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VMA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VMA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=1lwt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lwt OCA], [http://pdbe.org/1lwt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lwt RCSB], [http://www.ebi.ac.uk/pdbsum/1lwt 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=1lwt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lwt OCA], [http://pdbe.org/1lwt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lwt RCSB], [http://www.ebi.ac.uk/pdbsum/1lwt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lwt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<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=1lwt ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1lwt" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1lwt" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Endonuclease\|Endonuclease]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:48, 11 September 2015

OCA — Fri, 11 Sep 2015 15:48:16 GMT

←Older revision		Revision as of 15:48, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1lwt' size='340' side='right' caption='[[1lwt]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='1lwt' size='340' side='right' caption='[[1lwt]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lwt]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LWT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LWT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lwt]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LWT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LWT FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vde\|1vde]], [[1lws\|1lws]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vde\|1vde]], [[1lws\|1lws]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VMA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ~~Saccharomyces cerevisiae~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VMA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=1lwt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lwt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lwt RCSB], [http://www.ebi.ac.uk/pdbsum/1lwt 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=1lwt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lwt OCA], [http://pdbe.org/1lwt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lwt RCSB], [http://www.ebi.ac.uk/pdbsum/1lwt PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1lwt" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Saccharomyces cerevisiae~~]]	+	[[Category: Atcc 18824]]
	[[Category: Gimble, F S]]		[[Category: Gimble, F S]]
	[[Category: Moure, C M]]		[[Category: Moure, C M]]

OCA at 18:36, 25 December 2014

OCA — Thu, 25 Dec 2014 18:36:08 GMT

←Older revision		Revision as of 18:36, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1lwt]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LWT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LWT FirstGlance]. <br>		<table><tr><td colspan='2'>[[1lwt]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LWT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LWT FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vde\|1vde]], [[1lws\|1lws]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vde\|1vde]], [[1lws\|1lws]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VMA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VMA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=1lwt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lwt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lwt RCSB], [http://www.ebi.ac.uk/pdbsum/1lwt 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=1lwt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lwt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lwt RCSB], [http://www.ebi.ac.uk/pdbsum/1lwt PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VATA_YEAST VATA_YEAST]] Catalytic subunit of the peripheral V1 complex of vacuolar ATPase. V-ATPase (vacuolar ATPase) is responsible for acidifying a variety of intracellular compartments in eukaryotic cells. It is an electrogenic proton pump that generates a proton motive force of 180 mV, inside positive and acidic, in the vacuolar membrane vesicles. It may participate in maintenance of cytoplasmic Ca(2+) homeostasis. This is a catalytic subunit.<ref>PMID:1534148</ref> PI-SceI is an endonuclease that can cleave at a site present in a VMA1 allele that lacks the derived endonuclease segment of the open reading frame; cleavage at this site only occurs during meiosis and initiates "homing", a genetic event that converts a VMA1 allele lacking VDE into one that contains it.<ref>PMID:1534148</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Gimble, F S.]]	+	[[Category: Gimble, F S]]
-	[[Category: Moure, C M.]]	+	[[Category: Moure, C M]]
-	[[Category: Quiocho, F A.]]	+	[[Category: Quiocho, F A]]
	[[Category: Endonuclease]]		[[Category: Endonuclease]]
	[[Category: Homing endonuclease]]		[[Category: Homing endonuclease]]

OCA at 17:42, 28 September 2014

OCA — Sun, 28 Sep 2014 17:42:16 GMT

←Older revision		Revision as of 17:42, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1lwt.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the intein homing endonuclease PI-SceI bound to its substrate DNA (Ca2+ free)==
		+	<StructureSection load='1lwt' size='340' side='right' caption='[[1lwt]], [[Resolution\|resolution]] 3.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1lwt]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LWT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LWT FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vde\|1vde]], [[1lws\|1lws]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VMA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=1lwt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lwt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lwt RCSB], [http://www.ebi.ac.uk/pdbsum/1lwt 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/lw/1lwt_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 ==
		+	The first X-ray structures of an intein-DNA complex, that of the two-domain homing endonuclease PI-SceI bound to its 36-base pair DNA substrate, have been determined in the presence and absence of Ca(2+). The DNA shows an asymmetric bending pattern, with a major 50 degree bend in the endonuclease domain and a minor 22 degree bend in the splicing domain region. Distortions of the DNA bound to the endonuclease domain cause the insertion of the two cleavage sites in the catalytic center. DNA binding induces changes in the protein conformation. The two overlapping non-identical active sites in the endonucleolytic center contain two Ca(+2) ions that coordinate to the catalytic Asp residues. Structure analysis indicates that the top strand may be cleaved first.

-	~~{{STRUCTURE_1lwt\| PDB=1lwt \| SCENE= }}~~	+	Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence.,Moure CM, Gimble FS, Quiocho FA Nat Struct Biol. 2002 Oct;9(10):764-70. PMID:12219083<ref>PMID:12219083</ref>

-	~~===Crystal structure~~ of the ~~intein homing endonuclease PI-SceI bound to its substrate DNA (Ca2+ free)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12219083}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1lwt]] is a 3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1LWT OCA].~~	+

	==See Also==		==See Also==
	*[[Endonuclease\|Endonuclease]]		*[[Endonuclease\|Endonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012219083<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Gimble, F S.]]		[[Category: Gimble, F S.]]

OCA at 20:04, 20 October 2012

OCA — Sat, 20 Oct 2012 20:04:08 GMT

←Older revision		Revision as of 20:04, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1lwt]] is a 3 chain structure ~~of [[Endonuclease]]~~ with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LWT OCA].	+	[[1lwt]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LWT OCA].

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

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

OCA — Fri, 27 Jul 2012 09:18:53 GMT

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

←Older revision

Revision as of 09:18, 27 July 2012

OCA at 09:18, 27 July 2012

OCA — Fri, 27 Jul 2012 09:18:51 GMT

←Older revision		Revision as of 09:18, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1lwt.png\|left\|200px]]		[[Image:1lwt.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1lwt", 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_1lwt\| PDB=1lwt \| SCENE= }}		{{STRUCTURE_1lwt\| PDB=1lwt \| SCENE= }}

	===Crystal structure of the intein homing endonuclease PI-SceI bound to its substrate DNA (Ca2+ free)===		===Crystal structure of the intein homing endonuclease PI-SceI bound to its substrate DNA (Ca2+ free)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12219083}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12219083 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12219083}}		{{ABSTRACT_PUBMED_12219083}}

	==About this Structure==		==About this Structure==
-	~~1LWT~~ is a 3 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LWT OCA].	+	[[1lwt]] is a 3 chain structure of [[Endonuclease]] with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LWT OCA].
		+
		+	==See Also==
		+	*[[Endonuclease\|Endonuclease]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12219083~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012219083</ref><references group="xtra"/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Gimble, F S.]]		[[Category: Gimble, F S.]]
Line 30:		Line 21:
	[[Category: Endonuclease]]		[[Category: Endonuclease]]
	[[Category: Homing endonuclease]]		[[Category: Homing endonuclease]]
		+	[[Category: Hydrolase-dna complex]]
	[[Category: Intein]]		[[Category: Intein]]
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 02:40:39 2009''

OCA at 00:40, 18 February 2009

OCA — Wed, 18 Feb 2009 00:40:42 GMT

←Older revision		Revision as of 00:40, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1LWT is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LWT OCA].	+	1LWT is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LWT OCA].

	==Reference==		==Reference==
-	~~Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence., Moure CM, Gimble FS, Quiocho FA, Nat Struct Biol. 2002 Oct;9(10):764-70.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/12219083 12219083]~~	+	<ref group="xtra">PMID:12219083</ref><references group="xtra"/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Single protein]]
	[[Category: Gimble, F S.]]		[[Category: Gimble, F S.]]
	[[Category: Moure, C M.]]		[[Category: Moure, C M.]]
Line 34:		Line 33:
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jul 2 22~~:43:~~41 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 02:40:39 2009''