1nmz - Revision history

OCA at 07:57, 14 February 2024

OCA — Wed, 14 Feb 2024 07:57:51 GMT

←Older revision		Revision as of 07:57, 14 February 2024
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	<StructureSection load='1nmz' size='340' side='right'caption='[[1nmz]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='1nmz' size='340' side='right'caption='[[1nmz]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nmz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NMZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NMZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nmz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NMZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NMZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NYM:3-DEOXY-3-AMINOTHYMIDINE+MONOPHOSPHATE'>NYM</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]] 1.75Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/dTMP_kinase dTMP kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.9 2.7.4.9] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NYM:3-DEOXY-3-AMINOTHYMIDINE+MONOPHOSPHATE'>NYM</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nmz OCA], [https://pdbe.org/1nmz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nmz RCSB], [https://www.ebi.ac.uk/pdbsum/1nmz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nmz 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=1nmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nmz OCA], [https://pdbe.org/1nmz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nmz RCSB], [https://www.ebi.ac.uk/pdbsum/1nmz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nmz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/KTHY_HUMAN KTHY_HUMAN]] Catalyzes the conversion of dTMP to dTDP.	+	[https://www.uniprot.org/uniprot/KTHY_HUMAN KTHY_HUMAN] Catalyzes the conversion of dTMP to dTDP.
	== 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=1nmz 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=1nmz ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Nucleoside analogue prodrugs are dependent on efficient intracellular stepwise phosphorylation to their triphosphate form to become therapeutically active. In many cases it is this activation pathway that largely determines the efficacy of the drug. To gain further understanding of the determinants for efficient conversion by the enzyme thymidylate kinase (TMPK) of clinically important thymidine monophosphate analogues to the corresponding diphosphates, we solved the crystal structures of the enzyme, with either ADP or the ATP analogue AppNHp at the phosphoryl donor site, in complex with TMP, AZTMP (previous work), NH2TMP, d4TMP, ddTMP, and FLTMP (this work) at the phosphoryl acceptor site. In conjunction with steady-state kinetic data, our structures shed light on the effect of 3'-substitutions in the nucleoside monophosphate (NMP) sugar moiety on the catalytic rate. We observe a direct correlation between the rate of phosphorylation of an NMP and its ability to induce a closing of the enzyme's phosphate-binding loop (P-loop). Our results show the drastic effects that slight modifications of the substrates exert on the enzyme's conformation and, hence, activity and suggest the type of substitutions that are compatible with efficient phosphorylation by TMPK.
-
-	Structures of human thymidylate kinase in complex with prodrugs: implications for the structure-based design of novel compounds.,Ostermann N, Segura-Pena D, Meier C, Veit T, Monnerjahn C, Konrad M, Lavie A Biochemistry. 2003 Mar 11;42(9):2568-77. PMID:12614151<ref>PMID:12614151</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1nmz" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Thymidylate kinase 3D structures\|Thymidylate kinase 3D structures]]		*[[Thymidylate kinase 3D structures\|Thymidylate kinase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: DTMP kinase]]~~	+	[[Category: Konrad M]]
-	[[Category: Konrad, M]]	+	[[Category: Lavie A]]
-	[[Category: Lavie, A]]	+	[[Category: Meier C]]
-	[[Category: Meier, C]]	+	[[Category: Monnerjahn M]]
-	[[Category: Monnerjahn, M]]	+	[[Category: Ostermann N]]
-	[[Category: Ostermann, N]]	+	[[Category: Segura-Pena D]]
-	[[Category: Segura-Pena, D]]	+	[[Category: Veit T]]
-	[[Category: Veit, T]]	+
-	~~[[Category: Aminothymidine]]~~	+
-	~~[[Category: P-loop]]~~	+
-	~~[[Category: Thymidylate kinase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:56, 21 April 2021

OCA — Wed, 21 Apr 2021 08:56:32 GMT

←Older revision		Revision as of 08:56, 21 April 2021
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	<StructureSection load='1nmz' size='340' side='right'caption='[[1nmz]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='1nmz' size='340' side='right'caption='[[1nmz]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nmz]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NMZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1NMZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nmz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NMZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NMZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NYM:3-DEOXY-3-AMINOTHYMIDINE+MONOPHOSPHATE'>NYM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NYM:3-DEOXY-3-AMINOTHYMIDINE+MONOPHOSPHATE'>NYM</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/dTMP_kinase dTMP kinase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.9 2.7.4.9] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/dTMP_kinase dTMP kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.9 2.7.4.9] </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=1nmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nmz OCA], [~~http~~://pdbe.org/1nmz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1nmz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1nmz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1nmz 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=1nmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nmz OCA], [https://pdbe.org/1nmz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nmz RCSB], [https://www.ebi.ac.uk/pdbsum/1nmz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nmz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/KTHY_HUMAN KTHY_HUMAN]] Catalyzes the conversion of dTMP to dTDP.	+	[[https://www.uniprot.org/uniprot/KTHY_HUMAN KTHY_HUMAN]] Catalyzes the conversion of dTMP to dTDP.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Thymidylate kinase\|Thymidylate kinase]]	+	*[[Thymidylate kinase 3D structures\|Thymidylate kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:45, 17 July 2019

OCA — Wed, 17 Jul 2019 13:45:39 GMT

←Older revision		Revision as of 13:45, 17 July 2019
Line 1:		Line 1:

	==Crystal structure of human thymidylate kinase with NH2TMP and AppNHp==		==Crystal structure of human thymidylate kinase with NH2TMP and AppNHp==
-	<StructureSection load='1nmz' size='340' side='right' caption='[[1nmz]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='1nmz' size='340' side='right'caption='[[1nmz]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1nmz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NMZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1nmz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NMZ FirstGlance]. <br>
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nm/1nmz_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nm/1nmz_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 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1nmz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1nmz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Thymidylate kinase\|Thymidylate kinase]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: DTMP kinase]]		[[Category: DTMP kinase]]
	[[Category: Konrad, M]]		[[Category: Konrad, M]]

OCA at 12:16, 12 October 2017

OCA — Thu, 12 Oct 2017 12:16:13 GMT

←Older revision		Revision as of 12:16, 12 October 2017
Line 1:		Line 1:
		+
	==Crystal structure of human thymidylate kinase with NH2TMP and AppNHp==		==Crystal structure of human thymidylate kinase with NH2TMP and AppNHp==
	<StructureSection load='1nmz' size='340' side='right' caption='[[1nmz]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='1nmz' size='340' side='right' caption='[[1nmz]], [[Resolution\|resolution]] 1.75Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NYM:3-DEOXY-3-AMINOTHYMIDINE+MONOPHOSPHATE'>NYM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NYM:3-DEOXY-3-AMINOTHYMIDINE+MONOPHOSPHATE'>NYM</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTMP_kinase dTMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.9 2.7.4.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTMP_kinase dTMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.9 2.7.4.9] </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=1nmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nmz OCA], [http://pdbe.org/1nmz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nmz RCSB], [http://www.ebi.ac.uk/pdbsum/1nmz 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=1nmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nmz OCA], [http://pdbe.org/1nmz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nmz RCSB], [http://www.ebi.ac.uk/pdbsum/1nmz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nmz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1nmz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1nmz" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Thymidylate kinase\|Thymidylate kinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:40, 10 February 2016

OCA — Wed, 10 Feb 2016 05:40:28 GMT

←Older revision		Revision as of 05:40, 10 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=1nmz ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:54, 11 September 2015

OCA — Fri, 11 Sep 2015 05:54:35 GMT

←Older revision		Revision as of 05:54, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1nmz' size='340' side='right' caption='[[1nmz]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='1nmz' size='340' side='right' caption='[[1nmz]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nmz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NMZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nmz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NMZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NYM:3-DEOXY-3-AMINOTHYMIDINE+MONOPHOSPHATE'>NYM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NYM:3-DEOXY-3-AMINOTHYMIDINE+MONOPHOSPHATE'>NYM</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTMP_kinase dTMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.9 2.7.4.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTMP_kinase dTMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.9 2.7.4.9] </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=1nmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nmz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nmz RCSB], [http://www.ebi.ac.uk/pdbsum/1nmz 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=1nmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nmz OCA], [http://pdbe.org/1nmz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nmz RCSB], [http://www.ebi.ac.uk/pdbsum/1nmz PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 1nmz" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: DTMP kinase]]		[[Category: DTMP kinase]]
	[[Category: Konrad, M]]		[[Category: Konrad, M]]

OCA at 12:11, 25 December 2014

OCA — Thu, 25 Dec 2014 12:11:57 GMT

←Older revision		Revision as of 12:11, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1nmz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NMZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1nmz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NMZ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NYM:3-DEOXY-3-AMINOTHYMIDINE+MONOPHOSPHATE'>NYM</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NYM:3-DEOXY-3-AMINOTHYMIDINE+MONOPHOSPHATE'>NYM</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTMP_kinase dTMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.9 2.7.4.9] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTMP_kinase dTMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.9 2.7.4.9] </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=1nmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nmz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nmz RCSB], [http://www.ebi.ac.uk/pdbsum/1nmz 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=1nmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nmz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nmz RCSB], [http://www.ebi.ac.uk/pdbsum/1nmz PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KTHY_HUMAN KTHY_HUMAN]] Catalyzes the conversion of dTMP to dTDP.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: DTMP kinase]]		[[Category: DTMP kinase]]
-	[[Category: Konrad, M.]]	+	[[Category: Konrad, M]]
-	[[Category: Lavie, A.]]	+	[[Category: Lavie, A]]
-	[[Category: Meier, C.]]	+	[[Category: Meier, C]]
-	[[Category: Monnerjahn, M.]]	+	[[Category: Monnerjahn, M]]
-	[[Category: Ostermann, N.]]	+	[[Category: Ostermann, N]]
-	[[Category: Segura-Pena, D.]]	+	[[Category: Segura-Pena, D]]
-	[[Category: Veit, T.]]	+	[[Category: Veit, T]]
	[[Category: Aminothymidine]]		[[Category: Aminothymidine]]
	[[Category: P-loop]]		[[Category: P-loop]]
	[[Category: Thymidylate kinase]]		[[Category: Thymidylate kinase]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 14:09, 28 September 2014

OCA — Sun, 28 Sep 2014 14:09:52 GMT

←Older revision		Revision as of 14:09, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1nmz.~~png\|left~~\|200px]]	+	==Crystal structure of human thymidylate kinase with NH2TMP and AppNHp==
		+	<StructureSection load='1nmz' size='340' side='right' caption='[[1nmz]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1nmz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NMZ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NYM:3-DEOXY-3-AMINOTHYMIDINE+MONOPHOSPHATE'>NYM</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTMP_kinase dTMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.9 2.7.4.9] </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=1nmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nmz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nmz RCSB], [http://www.ebi.ac.uk/pdbsum/1nmz 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/nm/1nmz_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 ==
		+	Nucleoside analogue prodrugs are dependent on efficient intracellular stepwise phosphorylation to their triphosphate form to become therapeutically active. In many cases it is this activation pathway that largely determines the efficacy of the drug. To gain further understanding of the determinants for efficient conversion by the enzyme thymidylate kinase (TMPK) of clinically important thymidine monophosphate analogues to the corresponding diphosphates, we solved the crystal structures of the enzyme, with either ADP or the ATP analogue AppNHp at the phosphoryl donor site, in complex with TMP, AZTMP (previous work), NH2TMP, d4TMP, ddTMP, and FLTMP (this work) at the phosphoryl acceptor site. In conjunction with steady-state kinetic data, our structures shed light on the effect of 3'-substitutions in the nucleoside monophosphate (NMP) sugar moiety on the catalytic rate. We observe a direct correlation between the rate of phosphorylation of an NMP and its ability to induce a closing of the enzyme's phosphate-binding loop (P-loop). Our results show the drastic effects that slight modifications of the substrates exert on the enzyme's conformation and, hence, activity and suggest the type of substitutions that are compatible with efficient phosphorylation by TMPK.

-	~~{{STRUCTURE_1nmz\| PDB=1nmz \| SCENE= }}~~	+	Structures of human thymidylate kinase in complex with prodrugs: implications for the structure-based design of novel compounds.,Ostermann N, Segura-Pena D, Meier C, Veit T, Monnerjahn C, Konrad M, Lavie A Biochemistry. 2003 Mar 11;42(9):2568-77. PMID:12614151<ref>PMID:12614151</ref>

-	~~===Crystal structure~~ of ~~human thymidylate kinase with NH2TMP and AppNHp===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_12614151}}~~	+	==See Also==
-		+	*[[Thymidylate kinase\|Thymidylate kinase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1nmz~~]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NMZ OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:012614151<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: DTMP kinase]]		[[Category: DTMP kinase]]

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

OCA — Wed, 05 Dec 2012 21:31:09 GMT

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

←Older revision

Revision as of 21:31, 5 December 2012

OCA at 21:31, 5 December 2012

OCA — Wed, 05 Dec 2012 21:31:06 GMT

←Older revision		Revision as of 21:31, 5 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1nmz.png\|left\|200px]]		[[Image:1nmz.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1nmz", 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_1nmz\| PDB=1nmz \| SCENE= }}		{{STRUCTURE_1nmz\| PDB=1nmz \| SCENE= }}

	===Crystal structure of human thymidylate kinase with NH2TMP and AppNHp===		===Crystal structure of human thymidylate kinase with NH2TMP and AppNHp===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12614151}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12614151 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12614151}}		{{ABSTRACT_PUBMED_12614151}}

	==About this Structure==		==About this Structure==
-	~~1NMZ~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NMZ OCA].	+	[[1nmz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NMZ OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12614151~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012614151</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: DTMP kinase]]		[[Category: DTMP kinase]]
Line 36:		Line 24:
	[[Category: P-loop]]		[[Category: P-loop]]
	[[Category: Thymidylate kinase]]		[[Category: Thymidylate kinase]]
-		+	[[Category: Transferase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 15:51:47 2009''~~	+