2qq0 - Revision history

OCA at 09:17, 21 February 2024

2024-02-21T09:17:19Z

←Older revision		Revision as of 09:17, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='2qq0' size='340' side='right'caption='[[2qq0]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='2qq0' size='340' side='right'caption='[[2qq0]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qq0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_43589 Atcc 43589~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QQ0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QQ0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qq0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QQ0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QQ0 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</scene>, <scene name='pdbligand=TMP:THYMIDINE-5-PHOSPHATE'>TMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.5Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2qpo\|2qpo]], [[2qqe\|2qqe]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</scene>, <scene name='pdbligand=TMP:THYMIDINE-5-PHOSPHATE'>TMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tdk ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Thymidine_kinase Thymidine kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.21 2.7.1.21] </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=2qq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qq0 OCA], [https://pdbe.org/2qq0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qq0 RCSB], [https://www.ebi.ac.uk/pdbsum/2qq0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qq0 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=2qq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qq0 OCA], [https://pdbe.org/2qq0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qq0 RCSB], [https://www.ebi.ac.uk/pdbsum/2qq0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qq0 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/KITH_THEMA KITH_THEMA]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</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=2qq0 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=2qq0 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The human cytosolic thymidine kinase (TK) and structurally related TKs in prokaryotes play a crucial role in the synthesis and regulation of the cellular thymidine triphosphate pool. We report the crystal structures of the TK homotetramer from Thermotoga maritima in four different states: its apo-form, a binary complex with thymidine, as well as the ternary structures with the two substrates (thymidine/AppNHp) and the reaction products (TMP/ADP). In combination with fluorescence spectroscopy and mutagenesis experiments, our results demonstrate that ATP binding is linked to a substantial reorganization of the enzyme quaternary structure, leading to a transition from a closed, inactive conformation to an open, catalytic state. We hypothesize that these structural changes are relevant to enzyme function in situ as part of the catalytic cycle and serve an important role in regulating enzyme activity by amplifying the effects of feedback inhibitor binding.
-
-	Quaternary structure change as a mechanism for the regulation of thymidine kinase 1-like enzymes.,Segura-Pena D, Lichter J, Trani M, Konrad M, Lavie A, Lutz S Structure. 2007 Dec;15(12):1555-66. PMID:18073106<ref>PMID:18073106</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2qq0" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[Thymidine kinase\|Thymidine kinase]]	+	*[[Thymidine kinase 3D structures\|Thymidine kinase 3D structures]]
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 43589]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thymidine kinase~~]]	+	[[Category: Thermotoga maritima]]
-	[[Category: Konrad, M]]	+	[[Category: Konrad M]]
-	[[Category: Lavie, A]]	+	[[Category: Lavie A]]
-	[[Category: Lichter, J]]	+	[[Category: Lichter J]]
-	[[Category: Lutz, S]]	+	[[Category: Lutz S]]
-	[[Category: Segura-Pena, D]]	+	[[Category: Segura-Pena D]]
-	[[Category: Trani, M]]	+	[[Category: Trani M]]
-	~~[[Category: Appnhp]]~~	+
-	~~[[Category: Atp-binding]]~~	+
-	~~[[Category: Cytoplasm]]~~	+
-	~~[[Category: Dna synthesis]]~~	+
-	~~[[Category: Nucleotide-binding]]~~	+
-	~~[[Category: Open-conformation]]~~	+
-	~~[[Category: Tmtk]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:28, 25 June 2021

2021-06-25T08:28:48Z

←Older revision		Revision as of 08:28, 25 June 2021
Line 1:		Line 1:

	==Thymidine Kinase from Thermotoga Maritima in complex with thymidine + AppNHp==		==Thymidine Kinase from Thermotoga Maritima in complex with thymidine + AppNHp==
-	<StructureSection load='2qq0' size='340' side='right' caption='[[2qq0]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='2qq0' size='340' side='right'caption='[[2qq0]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qq0]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QQ0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2QQ0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qq0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QQ0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QQ0 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</scene>, <scene name='pdbligand=TMP:THYMIDINE-5-PHOSPHATE'>TMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</scene>, <scene name='pdbligand=TMP:THYMIDINE-5-PHOSPHATE'>TMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qpo\|2qpo]], [[2qqe\|2qqe]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2qpo\|2qpo]], [[2qqe\|2qqe]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tdk ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tdk ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Thymidine_kinase Thymidine kinase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.21 2.7.1.21] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Thymidine_kinase Thymidine kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.21 2.7.1.21] </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=2qq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qq0 OCA], [~~http~~://pdbe.org/2qq0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2qq0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2qq0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2qq0 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=2qq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qq0 OCA], [https://pdbe.org/2qq0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qq0 RCSB], [https://www.ebi.ac.uk/pdbsum/2qq0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qq0 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 43589]]		[[Category: Atcc 43589]]
		+	[[Category: Large Structures]]
	[[Category: Thymidine kinase]]		[[Category: Thymidine kinase]]
	[[Category: Konrad, M]]		[[Category: Konrad, M]]

OCA at 10:48, 5 September 2018

2018-09-05T10:48:12Z

←Older revision		Revision as of 10:48, 5 September 2018
Line 1:		Line 1:
		+
	==Thymidine Kinase from Thermotoga Maritima in complex with thymidine + AppNHp==		==Thymidine Kinase from Thermotoga Maritima in complex with thymidine + AppNHp==
	<StructureSection load='2qq0' size='340' side='right' caption='[[2qq0]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='2qq0' size='340' side='right' caption='[[2qq0]], [[Resolution\|resolution]] 1.50Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tdk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tdk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidine_kinase Thymidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.21 2.7.1.21] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidine_kinase Thymidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.21 2.7.1.21] </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=2qq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qq0 OCA], [http://pdbe.org/2qq0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qq0 RCSB], [http://www.ebi.ac.uk/pdbsum/2qq0 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=2qq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qq0 OCA], [http://pdbe.org/2qq0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qq0 RCSB], [http://www.ebi.ac.uk/pdbsum/2qq0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qq0 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qq/2qq0_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qq/2qq0_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 45:		Line 46:
	[[Category: Appnhp]]		[[Category: Appnhp]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
		+	[[Category: Cytoplasm]]
	[[Category: Dna synthesis]]		[[Category: Dna synthesis]]
	[[Category: Nucleotide-binding]]		[[Category: Nucleotide-binding]]

OCA at 12:30, 8 February 2016

2016-02-08T12:30:55Z

←Older revision		Revision as of 12:30, 8 February 2016
Line 17:		Line 17:
	<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=2qq0 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:35, 10 September 2015

2015-09-10T11:35:42Z

←Older revision		Revision as of 11:35, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2qq0' size='340' side='right' caption='[[2qq0]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='2qq0' size='340' side='right' caption='[[2qq0]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qq0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermotoga_maritima Thermotoga maritima~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QQ0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QQ0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qq0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QQ0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QQ0 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</scene>, <scene name='pdbligand=TMP:THYMIDINE-5-PHOSPHATE'>TMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</scene>, <scene name='pdbligand=TMP:THYMIDINE-5-PHOSPHATE'>TMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qpo\|2qpo]], [[2qqe\|2qqe]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qpo\|2qpo]], [[2qqe\|2qqe]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tdk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ~~Thermotoga maritima~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tdk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidine_kinase Thymidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.21 2.7.1.21] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidine_kinase Thymidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.21 2.7.1.21] </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=2qq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qq0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qq0 RCSB], [http://www.ebi.ac.uk/pdbsum/2qq0 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=2qq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qq0 OCA], [http://pdbe.org/2qq0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qq0 RCSB], [http://www.ebi.ac.uk/pdbsum/2qq0 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 27:
	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 2qq0" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Thermotoga maritima~~]]	+	[[Category: Atcc 43589]]
	[[Category: Thymidine kinase]]		[[Category: Thymidine kinase]]
	[[Category: Konrad, M]]		[[Category: Konrad, M]]

OCA at 16:12, 19 January 2015

2015-01-19T16:12:54Z

←Older revision		Revision as of 16:12, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2qq0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QQ0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QQ0 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2qq0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QQ0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QQ0 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</scene>, <scene name='pdbligand=TMP:THYMIDINE-5-PHOSPHATE'>TMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</scene>, <scene name='pdbligand=TMP:THYMIDINE-5-PHOSPHATE'>TMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qpo\|2qpo]], [[2qqe\|2qqe]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qpo\|2qpo]], [[2qqe\|2qqe]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tdk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 Thermotoga maritima])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tdk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 Thermotoga maritima])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidine_kinase Thymidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.21 2.7.1.21] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidine_kinase Thymidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.21 2.7.1.21] </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=2qq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qq0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qq0 RCSB], [http://www.ebi.ac.uk/pdbsum/2qq0 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=2qq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qq0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qq0 RCSB], [http://www.ebi.ac.uk/pdbsum/2qq0 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]
	[[Category: Thymidine kinase]]		[[Category: Thymidine kinase]]
-	[[Category: Konrad, M.]]	+	[[Category: Konrad, M]]
-	[[Category: Lavie, A.]]	+	[[Category: Lavie, A]]
-	[[Category: Lichter, J.]]	+	[[Category: Lichter, J]]
-	[[Category: Lutz, S.]]	+	[[Category: Lutz, S]]
-	[[Category: Segura-Pena, D.]]	+	[[Category: Segura-Pena, D]]
-	[[Category: Trani, M.]]	+	[[Category: Trani, M]]
	[[Category: Appnhp]]		[[Category: Appnhp]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
Line 47:		Line 47:
	[[Category: Nucleotide-binding]]		[[Category: Nucleotide-binding]]
	[[Category: Open-conformation]]		[[Category: Open-conformation]]
-	[[Category: Thymidine kinase]]
	[[Category: Tmtk]]		[[Category: Tmtk]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 08:22, 29 September 2014

2014-09-29T08:22:23Z

←Older revision		Revision as of 08:22, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2qq0.~~png~~\|~~left~~\|200px]]	+	==Thymidine Kinase from Thermotoga Maritima in complex with thymidine + AppNHp==
		+	<StructureSection load='2qq0' size='340' side='right' caption='[[2qq0]], [[Resolution\|resolution]] 1.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2qq0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QQ0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QQ0 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</scene>, <scene name='pdbligand=TMP:THYMIDINE-5-PHOSPHATE'>TMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qpo\|2qpo]], [[2qqe\|2qqe]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tdk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 Thermotoga maritima])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidine_kinase Thymidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.21 2.7.1.21] </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=2qq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qq0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qq0 RCSB], [http://www.ebi.ac.uk/pdbsum/2qq0 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/qq/2qq0_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 human cytosolic thymidine kinase (TK) and structurally related TKs in prokaryotes play a crucial role in the synthesis and regulation of the cellular thymidine triphosphate pool. We report the crystal structures of the TK homotetramer from Thermotoga maritima in four different states: its apo-form, a binary complex with thymidine, as well as the ternary structures with the two substrates (thymidine/AppNHp) and the reaction products (TMP/ADP). In combination with fluorescence spectroscopy and mutagenesis experiments, our results demonstrate that ATP binding is linked to a substantial reorganization of the enzyme quaternary structure, leading to a transition from a closed, inactive conformation to an open, catalytic state. We hypothesize that these structural changes are relevant to enzyme function in situ as part of the catalytic cycle and serve an important role in regulating enzyme activity by amplifying the effects of feedback inhibitor binding.

-	~~{{STRUCTURE_2qq0\| PDB=2qq0 \| SCENE= }}~~	+	Quaternary structure change as a mechanism for the regulation of thymidine kinase 1-like enzymes.,Segura-Pena D, Lichter J, Trani M, Konrad M, Lavie A, Lutz S Structure. 2007 Dec;15(12):1555-66. PMID:18073106<ref>PMID:18073106</ref>

-	~~===Thymidine Kinase from Thermotoga Maritima in complex with thymidine + AppNHp===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18073106}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2qq0]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermotoga_maritima Thermotoga maritima]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2QQ0 OCA].~~	+

	==See Also==		==See Also==
	*[[Thymidine kinase\|Thymidine kinase]]		*[[Thymidine kinase\|Thymidine kinase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018073106<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]
	[[Category: Thymidine kinase]]		[[Category: Thymidine kinase]]

OCA at 10:08, 20 October 2012

2012-10-20T10:08:36Z

←Older revision		Revision as of 10:08, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2qq0]] is a 2 chain structure ~~of [[Thymidine kinase]]~~ with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QQ0 OCA].	+	[[2qq0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QQ0 OCA].

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

OCA: Protected "2qq0" [edit=sysop:move=sysop]

2012-07-26T01:07:32Z

Protected "2qq0" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:07, 26 July 2012

OCA at 01:07, 26 July 2012

2012-07-26T01:07:30Z

←Older revision		Revision as of 01:07, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2qq0.png\|left\|200px]]		[[Image:2qq0.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2qq0", 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_2qq0\| PDB=2qq0 \| SCENE= }}		{{STRUCTURE_2qq0\| PDB=2qq0 \| SCENE= }}

	===Thymidine Kinase from Thermotoga Maritima in complex with thymidine + AppNHp===		===Thymidine Kinase from Thermotoga Maritima in complex with thymidine + AppNHp===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18073106}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18073106 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18073106}}		{{ABSTRACT_PUBMED_18073106}}

	==About this Structure==		==About this Structure==
-	~~2QQ0~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QQ0 OCA].	+	[[2qq0]] is a 2 chain structure of [[Thymidine kinase]] with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QQ0 OCA].
		+
		+	==See Also==
		+	*[[Thymidine kinase\|Thymidine kinase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18073106~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018073106</ref><references group="xtra"/>
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]
	[[Category: Thymidine kinase]]		[[Category: Thymidine kinase]]
Line 34:		Line 25:
	[[Category: Appnhp]]		[[Category: Appnhp]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
-	[[Category: Cytoplasm]]
	[[Category: Dna synthesis]]		[[Category: Dna synthesis]]
	[[Category: Nucleotide-binding]]		[[Category: Nucleotide-binding]]
Line 41:		Line 31:
	[[Category: Tmtk]]		[[Category: Tmtk]]
	[[Category: Transferase]]		[[Category: Transferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 22:01:15 2009''