2e1z - Revision history

OCA at 08:33, 25 October 2023

OCA — Wed, 25 Oct 2023 08:33:40 GMT

←Older revision		Revision as of 08:33, 25 October 2023
Line 3:		Line 3:
	<StructureSection load='2e1z' size='340' side='right'caption='[[2e1z]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='2e1z' size='340' side='right'caption='[[2e1z]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2e1z]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E1Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2e1z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E1Z FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=B4P:BIS(ADENOSINE)~~-~~5-TETRAPHOSPHATE'>B4P</scene>~~, ~~<scene name='pdbligand=EDO:~~1~~,2-ETHANEDIOL'>EDO</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]] 1.98Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1x3m\|1x3m]], [[1x3n\|1x3n]], [[2e1y\|2e1y]], [[2e20\|2e20]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Propionate_kinase Propionate kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.15 2.7.2.15]~~ </~~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=2e1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1z OCA], [https://pdbe.org/2e1z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e1z RCSB], [https://www.ebi.ac.uk/pdbsum/2e1z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e1z 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=2e1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1z OCA], [https://pdbe.org/2e1z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e1z RCSB], [https://www.ebi.ac.uk/pdbsum/2e1z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e1z ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/TDCD_SALTY TDCD_SALTY]] Catalyzes the conversion of propionyl phosphate and ADP to propionate and ATP. It can also use acetyl phosphate as phosphate group acceptor.[HAMAP-Rule:MF_01881]	+	[https://www.uniprot.org/uniprot/TDCD_SALTY TDCD_SALTY] Catalyzes the conversion of propionyl phosphate and ADP to propionate and ATP. It can also use acetyl phosphate as phosphate group acceptor.[HAMAP-Rule:MF_01881]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Propionate kinase~~]]	+	[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
-	[[Category: Murthy~~, M R.N~~]]	+	[[Category: Murthy MRN]]
-	[[Category: Savithri~~, H S~~]]	+	[[Category: Savithri HS]]
-	[[Category: Simanshu~~, D K]]~~	+	[[Category: Simanshu DK]]
-	~~[[Category: Acetate kinase]]~~	+
-	~~[[Category: Adp]]~~	+
-	~~[[Category: Amppnp]]~~	+
-	~~[[Category: Ap4a]]~~	+
-	~~[[Category: Atp]]~~	+
-	~~[[Category: Native]]~~	+
-	~~[[Category: Nucleotide]]~~	+
-	~~[[Category: Tdcd]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:49, 5 May 2021

OCA — Wed, 05 May 2021 09:49:52 GMT

←Older revision		Revision as of 09:49, 5 May 2021
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	<StructureSection load='2e1z' size='340' side='right'caption='[[2e1z]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='2e1z' size='340' side='right'caption='[[2e1z]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2e1z]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1Z OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2E1Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2e1z]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E1Z FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x3m\|1x3m]], [[1x3n\|1x3n]], [[2e1y\|2e1y]], [[2e20\|2e20]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1x3m\|1x3m]], [[1x3n\|1x3n]], [[2e1y\|2e1y]], [[2e20\|2e20]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Propionate_kinase Propionate kinase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.15 2.7.2.15] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Propionate_kinase Propionate kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.15 2.7.2.15] </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=2e1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1z OCA], [~~http~~://pdbe.org/2e1z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2e1z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2e1z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2e1z 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=2e1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1z OCA], [https://pdbe.org/2e1z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e1z RCSB], [https://www.ebi.ac.uk/pdbsum/2e1z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e1z ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/TDCD_SALTY TDCD_SALTY]] Catalyzes the conversion of propionyl phosphate and ADP to propionate and ATP. It can also use acetyl phosphate as phosphate group acceptor.[HAMAP-Rule:MF_01881]	+	[[https://www.uniprot.org/uniprot/TDCD_SALTY TDCD_SALTY]] Catalyzes the conversion of propionyl phosphate and ADP to propionate and ATP. It can also use acetyl phosphate as phosphate group acceptor.[HAMAP-Rule:MF_01881]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:09, 24 July 2019

OCA — Wed, 24 Jul 2019 09:09:21 GMT

←Older revision		Revision as of 09:09, 24 July 2019
Line 1:		Line 1:

	==Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with diadenosine tetraphosphate (Ap4A) obtained after co-crystallization with ATP==		==Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with diadenosine tetraphosphate (Ap4A) obtained after co-crystallization with ATP==
-	<StructureSection load='2e1z' size='340' side='right' caption='[[2e1z]], [[Resolution\|resolution]] 1.98Å' scene=''>	+	<StructureSection load='2e1z' size='340' side='right'caption='[[2e1z]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2e1z]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E1Z FirstGlance]. <br>		<table><tr><td colspan='2'>[[2e1z]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E1Z FirstGlance]. <br>
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/e1/2e1z_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e1/2e1z_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 34:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Propionate kinase]]		[[Category: Propionate kinase]]
	[[Category: Murthy, M R.N]]		[[Category: Murthy, M R.N]]

OCA at 13:13, 12 October 2017

OCA — Thu, 12 Oct 2017 13:13:43 GMT

←Older revision		Revision as of 13:13, 12 October 2017
Line 1:		Line 1:
		+
	==Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with diadenosine tetraphosphate (Ap4A) obtained after co-crystallization with ATP==		==Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with diadenosine tetraphosphate (Ap4A) obtained after co-crystallization with ATP==
	<StructureSection load='2e1z' size='340' side='right' caption='[[2e1z]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='2e1z' size='340' side='right' caption='[[2e1z]], [[Resolution\|resolution]] 1.98Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x3m\|1x3m]], [[1x3n\|1x3n]], [[2e1y\|2e1y]], [[2e20\|2e20]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x3m\|1x3m]], [[1x3n\|1x3n]], [[2e1y\|2e1y]], [[2e20\|2e20]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Propionate_kinase Propionate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.15 2.7.2.15] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Propionate_kinase Propionate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.15 2.7.2.15] </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=2e1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1z OCA], [http://pdbe.org/2e1z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e1z RCSB], [http://www.ebi.ac.uk/pdbsum/2e1z 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=2e1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1z OCA], [http://pdbe.org/2e1z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e1z RCSB], [http://www.ebi.ac.uk/pdbsum/2e1z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2e1z 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=2e1z ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 41:		Line 42:
	[[Category: Amppnp]]		[[Category: Amppnp]]
	[[Category: Ap4a]]		[[Category: Ap4a]]
		+	[[Category: Atp]]
	[[Category: Native]]		[[Category: Native]]
	[[Category: Nucleotide]]		[[Category: Nucleotide]]
	[[Category: Tdcd]]		[[Category: Tdcd]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 21:56, 11 September 2015

OCA — Fri, 11 Sep 2015 21:56:37 GMT

←Older revision		Revision as of 21:56, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2e1z' size='340' side='right' caption='[[2e1z]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='2e1z' size='340' side='right' caption='[[2e1z]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2e1z]] is a 1 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E1Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2e1z]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E1Z FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x3m\|1x3m]], [[1x3n\|1x3n]], [[2e1y\|2e1y]], [[2e20\|2e20]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x3m\|1x3m]], [[1x3n\|1x3n]], [[2e1y\|2e1y]], [[2e20\|2e20]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TdcD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 Salmonella enterica subsp. enterica serovar Typhimurium])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Propionate_kinase Propionate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.15 2.7.2.15] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Propionate_kinase Propionate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.15 2.7.2.15] </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=2e1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e1z RCSB], [http://www.ebi.ac.uk/pdbsum/2e1z 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=2e1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1z OCA], [http://pdbe.org/2e1z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e1z RCSB], [http://www.ebi.ac.uk/pdbsum/2e1z PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 2e1z" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Propionate kinase]]		[[Category: Propionate kinase]]
-	[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]
	[[Category: Murthy, M R.N]]		[[Category: Murthy, M R.N]]
	[[Category: Savithri, H S]]		[[Category: Savithri, H S]]

OCA at 20:07, 25 December 2014

OCA — Thu, 25 Dec 2014 20:07:00 GMT

←Older revision		Revision as of 20:07, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2e1z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E1Z FirstGlance]. <br>		<table><tr><td colspan='2'>[[2e1z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E1Z FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x3m\|1x3m]], [[1x3n\|1x3n]], [[2e1y\|2e1y]], [[2e20\|2e20]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x3m\|1x3m]], [[1x3n\|1x3n]], [[2e1y\|2e1y]], [[2e20\|2e20]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TdcD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 Salmonella enterica subsp. enterica serovar Typhimurium])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TdcD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 Salmonella enterica subsp. enterica serovar Typhimurium])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Propionate_kinase Propionate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.15 2.7.2.15] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Propionate_kinase Propionate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.15 2.7.2.15] </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=2e1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e1z RCSB], [http://www.ebi.ac.uk/pdbsum/2e1z 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=2e1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e1z RCSB], [http://www.ebi.ac.uk/pdbsum/2e1z PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TDCD_SALTY TDCD_SALTY]] Catalyzes the conversion of propionyl phosphate and ADP to propionate and ATP. It can also use acetyl phosphate as phosphate group acceptor.[HAMAP-Rule:MF_01881]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	[[Category: Propionate kinase]]		[[Category: Propionate kinase]]
	[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]		[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]
-	[[Category: Murthy, M R.N.]]	+	[[Category: Murthy, M R.N]]
-	[[Category: Savithri, H S.]]	+	[[Category: Savithri, H S]]
-	[[Category: Simanshu, D K.]]	+	[[Category: Simanshu, D K]]
	[[Category: Acetate kinase]]		[[Category: Acetate kinase]]
	[[Category: Adp]]		[[Category: Adp]]
Line 42:		Line 44:
	[[Category: Native]]		[[Category: Native]]
	[[Category: Nucleotide]]		[[Category: Nucleotide]]
-	[[Category: Propionate kinase]]
	[[Category: Tdcd]]		[[Category: Tdcd]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 01:44, 30 September 2014

OCA — Tue, 30 Sep 2014 01:44:36 GMT

←Older revision		Revision as of 01:44, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2e1z.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with diadenosine tetraphosphate (Ap4A) obtained after co-crystallization with ATP==
		+	<StructureSection load='2e1z' size='340' side='right' caption='[[2e1z]], [[Resolution\|resolution]] 1.98Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2e1z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E1Z FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x3m\|1x3m]], [[1x3n\|1x3n]], [[2e1y\|2e1y]], [[2e20\|2e20]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TdcD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 Salmonella enterica subsp. enterica serovar Typhimurium])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Propionate_kinase Propionate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.15 2.7.2.15] </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=2e1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e1z RCSB], [http://www.ebi.ac.uk/pdbsum/2e1z 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/e1/2e1z_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 ==
		+	Propionate kinase catalyses the last step in the anaerobic breakdown of L-threonine to propionate in which propionyl phosphate and ADP are converted to propionate and ATP. Here we report the structures of propionate kinase (TdcD) in the native form as well as in complex with diadenosine 5',5'''-P1,P4-tetraphosphate (Ap4A) by X-ray crystallography. Structure of TdcD obtained after cocrystallization with ATP showed Ap4A bound to the active site pocket suggesting the presence of Ap4A synthetic activity in TdcD. Binding of Ap4A to the enzyme was confirmed by the structure determination of a TdcD-Ap4A complex obtained after cocrystallization of TdcD with commercially available Ap4A. Mass spectroscopic studies provided further evidence for the formation of Ap4A by propionate kinase in the presence of ATP. In the TdcD-Ap4A complex structure, Ap4A is present in an extended conformation with one adenosine moiety present in the nucleotide binding site and other in the proposed propionate binding site. These observations tend to support direct in-line transfer of phosphoryl group during the kinase reaction.

-	~~{{STRUCTURE_2e1z\| PDB=2e1z \| SCENE= }}~~	+	Crystal structures of Salmonella typhimurium propionate kinase and its complex with Ap4A: evidence for a novel Ap4A synthetic activity.,Simanshu DK, Savithri HS, Murthy MR Proteins. 2008 Mar;70(4):1379-88. PMID:17894350<ref>PMID:17894350</ref>

-	~~===Crystal structure~~ of ~~Salmonella typhimurium propionate kinase (TdcD) in complex with diadenosine tetraphosphate (Ap4A) obtained after co-crystallization with ATP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17894350}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2e1z]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Salmonella_enterica_subsp~~.~~_enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2E1Z OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017894350<~~/~~ref~~><~~ref group="xtra">PMID:016139298</ref><ref group="xtra">PMID:016508089</ref><references group="xtra"~~/>	+
	[[Category: Propionate kinase]]		[[Category: Propionate kinase]]
	[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]		[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]

OCA at 12:28, 23 January 2013

OCA — Wed, 23 Jan 2013 12:28:29 GMT

←Older revision		Revision as of 12:28, 23 January 2013
Line 1:		Line 1:
	[[Image:2e1z.png\|left\|200px]]		[[Image:2e1z.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2e1z", 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_2e1z\| PDB=2e1z \| SCENE= }}		{{STRUCTURE_2e1z\| PDB=2e1z \| SCENE= }}

	===Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with diadenosine tetraphosphate (Ap4A) obtained after co-crystallization with ATP===		===Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with diadenosine tetraphosphate (Ap4A) obtained after co-crystallization with ATP===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17894350}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17894350 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17894350}}		{{ABSTRACT_PUBMED_17894350}}

Line 22:		Line 11:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17894350~~</ref><ref group="xtra">PMID:~~16139298~~</ref><ref group="xtra">PMID:~~16508089~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017894350</ref><ref group="xtra">PMID:016139298</ref><ref group="xtra">PMID:016508089</ref><references group="xtra"/>
	[[Category: Propionate kinase]]		[[Category: Propionate kinase]]
	[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]		[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]
Line 32:		Line 21:
	[[Category: Amppnp]]		[[Category: Amppnp]]
	[[Category: Ap4a]]		[[Category: Ap4a]]
-	[[Category: Atp]]
	[[Category: Native]]		[[Category: Native]]
	[[Category: Nucleotide]]		[[Category: Nucleotide]]

OCA: Protected "2e1z" [edit=sysop:move=sysop]

OCA — Mon, 14 Mar 2011 21:48:13 GMT

Protected "2e1z" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:48, 14 March 2011

OCA at 21:48, 14 March 2011

OCA — Mon, 14 Mar 2011 21:48:11 GMT

←Older revision		Revision as of 21:48, 14 March 2011
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2e1z.png\|left\|200px]]		[[Image:2e1z.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	~~2E1Z~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/~~Salmonella_typhimurium~~ Salmonella typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1Z OCA].	+	[[2e1z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1Z OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:17894350</ref><ref group="xtra">PMID:16139298</ref><ref group="xtra">PMID:16508089</ref><references group="xtra"/>		<ref group="xtra">PMID:17894350</ref><ref group="xtra">PMID:16139298</ref><ref group="xtra">PMID:16508089</ref><references group="xtra"/>
	[[Category: Propionate kinase]]		[[Category: Propionate kinase]]
-	[[Category: Salmonella typhimurium]]	+	[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]
	[[Category: Murthy, M R.N.]]		[[Category: Murthy, M R.N.]]
	[[Category: Savithri, H S.]]		[[Category: Savithri, H S.]]
Line 39:		Line 38:
	[[Category: Tdcd]]		[[Category: Tdcd]]
	[[Category: Transferase]]		[[Category: Transferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 05:38:51 2009''