1t3m - Revision history

OCA at 06:25, 23 August 2023

OCA — Wed, 23 Aug 2023 06:25:19 GMT

←Older revision		Revision as of 06:25, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='1t3m' size='340' side='right'caption='[[1t3m]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='1t3m' size='340' side='right'caption='[[1t3m]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t3m]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1T3M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t3m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T3M FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NA:SODIUM+ION'>NA</scene>~~, ~~<scene name='pdbligand=NO3:NITRATE+ION'>NO3</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]] 1.65Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1jn9\|1jn9]], [[1k2x\|1k2x]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>YBIK, B0828 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])</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=1t3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3m OCA], [https://pdbe.org/1t3m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t3m RCSB], [https://www.ebi.ac.uk/pdbsum/1t3m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t3m 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/Asparaginase Asparaginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.1 3.5.1.1]~~ </~~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=1t3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3m OCA], [~~http~~://pdbe.org/1t3m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1t3m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1t3m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1t3m ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/IAAA_ECOLI IAAA_ECOLI]] Degrades proteins damaged by L-isoaspartyl residue formation (also known as beta-Asp residues). Degrades L-isoaspartyl-containing di- and maybe also tripeptides. Also has L-asparaginase activity, although this may not be its principal function.<ref>PMID:11988085</ref> May be involved in glutathione, and possibly other peptide, transport, although these results could also be due to polar effects of disruption.<ref>PMID:11988085</ref>	+	[https://www.uniprot.org/uniprot/IAAA_ECOLI IAAA_ECOLI] Degrades proteins damaged by L-isoaspartyl residue formation (also known as beta-Asp residues). Degrades L-isoaspartyl-containing di- and maybe also tripeptides. Also has L-asparaginase activity, although this may not be its principal function.<ref>PMID:11988085</ref> May be involved in glutathione, and possibly other peptide, transport, although these results could also be due to polar effects of disruption.<ref>PMID:11988085</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895]]~~	+	[[Category: Escherichia coli]]
-	~~[[Category: Asparaginase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hejazi, M]]	+	[[Category: Hejazi M]]
-	[[Category: Lockau, W]]	+	[[Category: Lockau W]]
-	[[Category: Lubkowski, J]]	+	[[Category: Lubkowski J]]
-	[[Category: Pazgier, M]]	+	[[Category: Pazgier M]]
-	[[Category: Prahl, A]]	+	[[Category: Prahl A]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Isoaspartyl peptidase]]~~	+
-	~~[[Category: Plant-type asparaginase]]~~	+
-	~~[[Category: Type iii l-asparaginase~~]]	+

OCA at 11:41, 24 December 2020

OCA — Thu, 24 Dec 2020 11:41:16 GMT

←Older revision		Revision as of 11:41, 24 December 2020
Line 1:		Line 1:

	==Structure of the isoaspartyl peptidase with L-asparaginase activity from E. coli==		==Structure of the isoaspartyl peptidase with L-asparaginase activity from E. coli==
-	<StructureSection load='1t3m' size='340' side='right' caption='[[1t3m]], [[Resolution\|resolution]] 1.65Å' scene=''>	+	<StructureSection load='1t3m' size='340' side='right'caption='[[1t3m]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t3m]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3M OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1T3M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t3m]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3M OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1T3M FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jn9\|1jn9]], [[1k2x\|1k2x]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1jn9\|1jn9]], [[1k2x\|1k2x]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YBIK, B0828 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YBIK, B0828 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Asparaginase Asparaginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.1 3.5.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Asparaginase Asparaginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.1 3.5.1.1] </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=1t3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3m OCA], [http://pdbe.org/1t3m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t3m RCSB], [http://www.ebi.ac.uk/pdbsum/1t3m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t3m 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=1t3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3m OCA], [http://pdbe.org/1t3m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t3m RCSB], [http://www.ebi.ac.uk/pdbsum/1t3m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t3m ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 37:		Line 37:
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Asparaginase]]		[[Category: Asparaginase]]
		+	[[Category: Large Structures]]
	[[Category: Hejazi, M]]		[[Category: Hejazi, M]]
	[[Category: Lockau, W]]		[[Category: Lockau, W]]

OCA at 07:29, 14 March 2018

OCA — Wed, 14 Mar 2018 07:29:36 GMT

←Older revision		Revision as of 07:29, 14 March 2018
Line 1:		Line 1:
		+
	==Structure of the isoaspartyl peptidase with L-asparaginase activity from E. coli==		==Structure of the isoaspartyl peptidase with L-asparaginase activity from E. coli==
	<StructureSection load='1t3m' size='340' side='right' caption='[[1t3m]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='1t3m' size='340' side='right' caption='[[1t3m]], [[Resolution\|resolution]] 1.65Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YBIK, B0828 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YBIK, B0828 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Asparaginase Asparaginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.1 3.5.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Asparaginase Asparaginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.1 3.5.1.1] </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=1t3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3m OCA], [http://pdbe.org/1t3m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t3m RCSB], [http://www.ebi.ac.uk/pdbsum/1t3m 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=1t3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3m OCA], [http://pdbe.org/1t3m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t3m RCSB], [http://www.ebi.ac.uk/pdbsum/1t3m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t3m ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t3/1t3m_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t3/1t3m_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>

OCA at 16:15, 7 February 2016

OCA — Sun, 07 Feb 2016 16:15:47 GMT

←Older revision		Revision as of 16:15, 7 February 2016
Line 19:		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=1t3m ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 03:08, 10 September 2015

OCA — Thu, 10 Sep 2015 03:08:30 GMT

←Older revision		Revision as of 03:08, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1t3m' size='340' side='right' caption='[[1t3m]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='1t3m' size='340' side='right' caption='[[1t3m]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t3m]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T3M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t3m]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T3M FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jn9\|1jn9]], [[1k2x\|1k2x]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jn9\|1jn9]], [[1k2x\|1k2x]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YBIK, B0828 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YBIK, B0828 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Asparaginase Asparaginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.1 3.5.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Asparaginase Asparaginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.1 3.5.1.1] </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=1t3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t3m RCSB], [http://www.ebi.ac.uk/pdbsum/1t3m 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=1t3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3m OCA], [http://pdbe.org/1t3m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t3m RCSB], [http://www.ebi.ac.uk/pdbsum/1t3m PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~ASGX_ECOLI ASGX_ECOLI~~]] Degrades proteins damaged by L-isoaspartyl residue formation (also known as beta-Asp residues). Degrades L-isoaspartyl-containing di- and maybe also tripeptides. Also has L-asparaginase activity, although this may not be its principal function.<ref>PMID:11988085~~</ref> <ref>PMID:12007658~~</ref> May be involved in glutathione, and possibly other peptide, transport, although these results could also be due to polar effects of disruption.<ref>PMID:11988085~~</ref> <ref>PMID:12007658~~</ref>	+	[[http://www.uniprot.org/uniprot/IAAA_ECOLI IAAA_ECOLI]] Degrades proteins damaged by L-isoaspartyl residue formation (also known as beta-Asp residues). Degrades L-isoaspartyl-containing di- and maybe also tripeptides. Also has L-asparaginase activity, although this may not be its principal function.<ref>PMID:11988085</ref> May be involved in glutathione, and possibly other peptide, transport, although these results could also be due to polar effects of disruption.<ref>PMID:11988085</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 29:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1t3m" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: Asparaginase]]		[[Category: Asparaginase]]
-	[[Category: Escherichia coli]]
	[[Category: Hejazi, M]]		[[Category: Hejazi, M]]
	[[Category: Lockau, W]]		[[Category: Lockau, W]]

OCA at 16:36, 24 December 2014

OCA — Wed, 24 Dec 2014 16:36:39 GMT

←Older revision		Revision as of 16:36, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1t3m]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T3M FirstGlance]. <br>		<table><tr><td colspan='2'>[[1t3m]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T3M FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jn9\|1jn9]], [[1k2x\|1k2x]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jn9\|1jn9]], [[1k2x\|1k2x]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YBIK, B0828 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YBIK, B0828 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Asparaginase Asparaginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.1 3.5.1.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Asparaginase Asparaginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.1 3.5.1.1] </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=1t3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t3m RCSB], [http://www.ebi.ac.uk/pdbsum/1t3m 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=1t3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t3m RCSB], [http://www.ebi.ac.uk/pdbsum/1t3m PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ASGX_ECOLI ASGX_ECOLI]] Degrades proteins damaged by L-isoaspartyl residue formation (also known as beta-Asp residues). Degrades L-isoaspartyl-containing di- and maybe also tripeptides. Also has L-asparaginase activity, although this may not be its principal function.<ref>PMID:11988085</ref> <ref>PMID:12007658</ref> May be involved in glutathione, and possibly other peptide, transport, although these results could also be due to polar effects of disruption.<ref>PMID:11988085</ref> <ref>PMID:12007658</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	[[Category: Asparaginase]]		[[Category: Asparaginase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Hejazi, M.]]	+	[[Category: Hejazi, M]]
-	[[Category: Lockau, W.]]	+	[[Category: Lockau, W]]
-	[[Category: Lubkowski, J.]]	+	[[Category: Lubkowski, J]]
-	[[Category: Pazgier, M.]]	+	[[Category: Pazgier, M]]
-	[[Category: Prahl, A.]]	+	[[Category: Prahl, A]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Isoaspartyl peptidase]]		[[Category: Isoaspartyl peptidase]]
	[[Category: Plant-type asparaginase]]		[[Category: Plant-type asparaginase]]
	[[Category: Type iii l-asparaginase]]		[[Category: Type iii l-asparaginase]]

OCA at 21:45, 29 September 2014

OCA — Mon, 29 Sep 2014 21:45:12 GMT

←Older revision		Revision as of 21:45, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1t3m.~~png~~\|~~left~~\|200px]]	+	==Structure of the isoaspartyl peptidase with L-asparaginase activity from E. coli==
		+	<StructureSection load='1t3m' size='340' side='right' caption='[[1t3m]], [[Resolution\|resolution]] 1.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1t3m]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T3M FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jn9\|1jn9]], [[1k2x\|1k2x]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YBIK, B0828 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Asparaginase Asparaginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.1 3.5.1.1] </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=1t3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t3m RCSB], [http://www.ebi.ac.uk/pdbsum/1t3m 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/t3/1t3m_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 crystal structure of the Escherichia coli enzyme (EcAIII) with isoaspartyl dipeptidase and L-asparaginase activity has been solved and refined to a resolution of 1.65 angstroms, with crystallographic R-factor and Rfree values of 0.178 and 0.209, respectively. EcAIII belongs to the family of N-terminal hydrolases. The amino-acid sequence of EcAIII is homologous to those of putative asparaginases from plants. The structure of EcAIII is similar to the structures of glycosylasparaginases. The mature and catalytically active form of EcAIII is a heterotetramer consisting of two alpha-subunits and two beta-subunits. Both of the equivalent active sites present in the EcAIII tetramer is assisted by a metal-binding site. The metal cations, modelled here as Na+, have not previously been observed in glycosylasparaginases. This reported structure helps to explain the inability of EcAIII and other plant-type asparaginases to hydrolyze N4-(beta-N-acetylglucosaminyl)-L-asparagine, the substrate of glycosylasparaginases.

-	~~{{STRUCTURE_1t3m\| PDB=1t3m \| SCENE= }}~~	+	Structure of the isoaspartyl peptidase with L-asparaginase activity from Escherichia coli.,Prahl A, Pazgier M, Hejazi M, Lockau W, Lubkowski J Acta Crystallogr D Biol Crystallogr. 2004 Jun;60(Pt 6):1173-6. Epub 2004, May 21. PMID:15159592<ref>PMID:15159592</ref>

-	~~===Structure~~ of the ~~isoaspartyl peptidase with L-asparaginase activity from E~~. ~~coli===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15159592}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1t3m]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3M OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015159592<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Asparaginase]]		[[Category: Asparaginase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

OCA: Protected "1t3m" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 13:12:47 GMT

Protected "1t3m" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:12, 5 January 2013

OCA at 13:12, 5 January 2013

OCA — Sat, 05 Jan 2013 13:12:45 GMT

←Older revision		Revision as of 13:12, 5 January 2013
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-	{{Seed}}
	[[Image:1t3m.png\|left\|200px]]		[[Image:1t3m.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1t3m", 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.
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	{{STRUCTURE_1t3m\| PDB=1t3m \| SCENE= }}		{{STRUCTURE_1t3m\| PDB=1t3m \| SCENE= }}

	===Structure of the isoaspartyl peptidase with L-asparaginase activity from E. coli===		===Structure of the isoaspartyl peptidase with L-asparaginase activity from E. coli===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15159592}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15159592 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15159592}}		{{ABSTRACT_PUBMED_15159592}}

	==About this Structure==		==About this Structure==
-	~~1T3M~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3M OCA].	+	[[1t3m]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3M OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15159592~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015159592</ref><references group="xtra"/>
	[[Category: Asparaginase]]		[[Category: Asparaginase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
Line 31:		Line 19:
	[[Category: Pazgier, M.]]		[[Category: Pazgier, M.]]
	[[Category: Prahl, A.]]		[[Category: Prahl, A.]]
		+	[[Category: Hydrolase]]
	[[Category: Isoaspartyl peptidase]]		[[Category: Isoaspartyl peptidase]]
	[[Category: Plant-type asparaginase]]		[[Category: Plant-type asparaginase]]
	[[Category: Type iii l-asparaginase]]		[[Category: Type iii l-asparaginase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 15:02:24 2009''

OCA at 13:02, 16 February 2009

OCA — Mon, 16 Feb 2009 13:02:25 GMT

←Older revision		Revision as of 13:02, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1T3M is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3M OCA].	+	1T3M is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3M OCA].

	==Reference==		==Reference==
-	Structure of the isoaspartyl peptidase with L-asparaginase activity from Escherichia coli., Prahl A, Pazgier M, Hejazi M, Lockau W, Lubkowski J, Acta Crystallogr D Biol Crystallogr. 2004 Jun;60(Pt 6):1173-6. Epub 2004, May 21. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15159592 15159592]~~	+	<ref group="xtra">PMID:15159592</ref><references group="xtra"/>
	[[Category: Asparaginase]]		[[Category: Asparaginase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Protein complex]]
	[[Category: Hejazi, M.]]		[[Category: Hejazi, M.]]
	[[Category: Lockau, W.]]		[[Category: Lockau, W.]]
Line 36:		Line 35:
	[[Category: Type iii l-asparaginase]]		[[Category: Type iii l-asparaginase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 17~~:49:~~57 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 15:02:24 2009''