5tmp - Revision history

OCA at 00:56, 28 December 2023

2023-12-28T00:56:22Z

← Older revision		Revision as of 00:56, 28 December 2023
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	<StructureSection load='5tmp' size='340' side='right'caption='[[5tmp]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='5tmp' size='340' side='right'caption='[[5tmp]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5tmp]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TMP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5TMP FirstGlance]. <br>		<table><tr><td colspan='2'>[[5tmp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TMP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TMP FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=Z5A:P1~~-~~(5-ADENOSYL)P5-(5-(3AZIDO-3-DEOXYTHYMIDYL))PENTAPHOSPHATE'>Z5A</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='~~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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=Z5A:P1-(5-ADENOSYL)P5-(5-(3AZIDO-3-DEOXYTHYMIDYL))PENTAPHOSPHATE'>Z5A</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5tmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tmp OCA], [~~http~~://pdbe.org/5tmp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5tmp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5tmp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5tmp 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=5tmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tmp OCA], [https://pdbe.org/5tmp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tmp RCSB], [https://www.ebi.ac.uk/pdbsum/5tmp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tmp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/KTHY_ECOLI KTHY_ECOLI]] Catalyzes the reversible phosphorylation of deoxythymidine monophosphate (dTMP) to deoxythymidine diphosphate (dTDP), using ATP as its preferred phosphoryl donor. Situated at the junction of both de novo and salvage pathways of deoxythymidine triphosphate (dTTP) synthesis, is essential for DNA synthesis and cellular growth.		[https://www.uniprot.org/uniprot/KTHY_ECOLI KTHY_ECOLI] Catalyzes the reversible phosphorylation of deoxythymidine monophosphate (dTMP) to deoxythymidine diphosphate (dTDP), using ATP as its preferred phosphoryl donor. Situated at the junction of both de novo and salvage pathways of deoxythymidine triphosphate (dTTP) synthesis, is essential for DNA synthesis and cellular growth.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]		[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: DTMP kinase]]~~		[[Category: Lavie A]]
	[[Category: Lavie, A]]		[[Category: Ostermann N]]
	[[Category: Ostermann, N]]		[[Category: Schlichting I]]
	[[Category: Schlichting, I]]
	~~[[Category: Atp:dtmp phosphotransferase]]~~
	~~[[Category: Transferase~~]]

OCA at 12:14, 23 September 2020

2020-09-23T12:14:11Z

← Older revision		Revision as of 12:14, 23 September 2020
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	==COMPLEX OF E. COLI THYMIDYLATE KINASE WITH THE BISUBSTRATE INHIBITOR AZTP5A==		==COMPLEX OF E. COLI THYMIDYLATE KINASE WITH THE BISUBSTRATE INHIBITOR AZTP5A==
	<StructureSection load='5tmp' size='340' side='right' caption='[[5tmp]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='5tmp' size='340' side='right'caption='[[5tmp]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5tmp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TMP OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TMP FirstGlance]. <br>		<table><tr><td colspan='2'>[[5tmp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TMP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5TMP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=Z5A:P1-(5-ADENOSYL)P5-(5-(3AZIDO-3-DEOXYTHYMIDYL))PENTAPHOSPHATE'>Z5A</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=Z5A:P1-(5-ADENOSYL)P5-(5-(3AZIDO-3-DEOXYTHYMIDYL))PENTAPHOSPHATE'>Z5A</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=5tmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tmp OCA], [http://pdbe.org/5tmp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tmp RCSB], [http://www.ebi.ac.uk/pdbsum/5tmp PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5tmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tmp OCA], [http://pdbe.org/5tmp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tmp RCSB], [http://www.ebi.ac.uk/pdbsum/5tmp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tmp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tm/5tmp_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tm/5tmp_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>
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	==See Also==		==See Also==
	*[[Thymidylate kinase\|Thymidylate kinase]]		*[[Thymidylate kinase 3D structures\|Thymidylate kinase 3D structures]]
	*[[Thymidylate synthase\|Thymidylate synthase]]		*[[Thymidylate synthase 3D structures\|Thymidylate synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
			[[Category: Large Structures]]
	[[Category: DTMP kinase]]		[[Category: DTMP kinase]]
	[[Category: Lavie, A]]		[[Category: Lavie, A]]

OCA at 08:08, 7 February 2016

2016-02-07T08:08:42Z

← Older revision		Revision as of 08:08, 7 February 2016
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	<StructureSection load='5tmp' size='340' side='right' caption='[[5tmp]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='5tmp' size='340' side='right' caption='[[5tmp]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5tmp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TMP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TMP FirstGlance]. <br>		<table><tr><td colspan='2'>[[5tmp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TMP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TMP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=Z5A:P1-(5-ADENOSYL)P5-(5-(3AZIDO-3-DEOXYTHYMIDYL))PENTAPHOSPHATE'>Z5A</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=Z5A:P1-(5-ADENOSYL)P5-(5-(3AZIDO-3-DEOXYTHYMIDYL))PENTAPHOSPHATE'>Z5A</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=5tmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tmp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5tmp RCSB], [http://www.ebi.ac.uk/pdbsum/5tmp 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=5tmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tmp OCA], [http://pdbe.org/5tmp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tmp RCSB], [http://www.ebi.ac.uk/pdbsum/5tmp PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	<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=5tmp ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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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 5tmp" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Escherichia~~ coli]]		[[Category: Bacillus coli migula 1895]]
	[[Category: DTMP kinase]]		[[Category: DTMP kinase]]
	[[Category: Lavie, A]]		[[Category: Lavie, A]]

OCA at 13:34, 24 December 2014

2014-12-24T13:34:15Z

← Older revision		Revision as of 13:34, 24 December 2014
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	<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=5tmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tmp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5tmp RCSB], [http://www.ebi.ac.uk/pdbsum/5tmp 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=5tmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tmp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5tmp RCSB], [http://www.ebi.ac.uk/pdbsum/5tmp PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/KTHY_ECOLI KTHY_ECOLI]] Catalyzes the reversible phosphorylation of deoxythymidine monophosphate (dTMP) to deoxythymidine diphosphate (dTDP), using ATP as its preferred phosphoryl donor. Situated at the junction of both de novo and salvage pathways of deoxythymidine triphosphate (dTTP) synthesis, is essential for DNA synthesis and cellular growth.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 16:47, 10 December 2014

2014-12-10T16:47:35Z

← Older revision		Revision as of 16:47, 10 December 2014
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	[[Image:~~5tmp~~.~~png~~\|~~left~~\|~~200px~~]]		==COMPLEX OF E. COLI THYMIDYLATE KINASE WITH THE BISUBSTRATE INHIBITOR AZTP5A==
			<StructureSection load='5tmp' size='340' side='right' caption='[[5tmp]], [[Resolution\|resolution]] 1.98Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[5tmp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TMP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TMP FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=Z5A:P1-(5-ADENOSYL)P5-(5-(3AZIDO-3-DEOXYTHYMIDYL))PENTAPHOSPHATE'>Z5A</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='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=5tmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tmp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5tmp RCSB], [http://www.ebi.ac.uk/pdbsum/5tmp 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/tm/5tmp_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The crystal structures of Escherichia coli thymidylate kinase (TmpK) in complex with P1-(5'-adenosyl)-P5-(5'-thymidyl)pentaphosphate and P1-(5'-adenosyl)P5-[5'-(3'-azido-3'-deoxythymidine)] pentaphosphate have been solved to 2.0-A and 2.2-A resolution, respectively. The overall structure of the bacterial TmpK is very similar to that of yeast TmpK. In contrast to the human and yeast TmpKs, which phosphorylate 3'-azido-3'-deoxythymidine 5'-monophosphate (AZT-MP) at a 200-fold reduced turnover number (kcat) in comparison to the physiological substrate dTMP, reduction of kcat is only 2-fold for the bacterial enzyme. The different kinetic properties toward AZT-MP between the eukaryotic TmpKs and E. coli TmpK can be rationalized by the different ways in which these enzymes stabilize the presumed transition state and the different manner in which a carboxylic acid side chain in the P loop interacts with the deoxyribose of the monophosphate. Yeast TmpK interacts with the 3'-hydroxyl of dTMP through Asp-14 of the P loop in a bidentate manner: binding of AZT-MP results in a shift of the P loop to accommodate the larger substituent. In E. coli TmpK, the corresponding residue is Glu-12, and it interacts in a side-on fashion with the 3'-hydroxyl of dTMP. This different mode of interaction between the P loop carboxylic acid with the 3' substituent of the monophosphate deoxyribose allows the accommodation of an azido group in the case of the E. coli enzyme without significant P loop movement. In addition, although the yeast enzyme uses Arg-15 (a glycine in E. coli) to stabilize the transition state, E. coli seems to use Arg-153 from a region termed Lid instead. Thus, the binding of AZT-MP to the yeast TmpK results in the shift of a catalytic residue, which is not the case for the bacterial kinase.

	~~{{STRUCTURE_5tmp\| PDB=5tmp \| SCENE= }}~~		Structural basis for efficient phosphorylation of 3'-azidothymidine monophosphate by Escherichia coli thymidylate kinase.,Lavie A, Ostermann N, Brundiers R, Goody RS, Reinstein J, Konrad M, Schlichting I Proc Natl Acad Sci U S A. 1998 Nov 24;95(24):14045-50. PMID:9826650<ref>PMID:9826650</ref>

	~~===COMPLEX OF E. COLI THYMIDYLATE KINASE WITH THE BISUBSTRATE INHIBITOR AZTP5A===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_9826650}}~~

	~~==About this Structure==~~
	~~[[5tmp]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=5TMP OCA].~~

	==See Also==		==See Also==
			*[[Thymidylate kinase\|Thymidylate kinase]]
	*[[Thymidylate synthase\|Thymidylate synthase]]		*[[Thymidylate synthase\|Thymidylate synthase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:009826650<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: DTMP kinase]]		[[Category: DTMP kinase]]
	[[Category: Lavie, A.]]		[[Category: Lavie, A]]
	[[Category: Ostermann, N.]]		[[Category: Ostermann, N]]
	[[Category: Schlichting, I.]]		[[Category: Schlichting, I]]
	[[Category: Atp:dtmp phosphotransferase]]		[[Category: Atp:dtmp phosphotransferase]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 06:04, 20 October 2012

2012-10-20T06:04:12Z

← Older revision		Revision as of 06:04, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[5tmp]] is a 1 chain structure ~~of [[Thymidylate synthase]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TMP OCA].		[[5tmp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TMP OCA].

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

OCA: Protected "5tmp" [edit=sysop:move=sysop]

2012-07-25T12:01:23Z

Protected "5tmp" [edit=sysop:move=sysop]

← Older revision	Revision as of 12:01, 25 July 2012
(No difference)

OCA at 12:01, 25 July 2012

2012-07-25T12:01:20Z

← Older revision		Revision as of 12:01, 25 July 2012
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	{{STRUCTURE_5tmp\| PDB=5tmp \| SCENE= }}		{{STRUCTURE_5tmp\| PDB=5tmp \| SCENE= }}

	===COMPLEX OF E. COLI THYMIDYLATE KINASE WITH THE BISUBSTRATE INHIBITOR AZTP5A===		===COMPLEX OF E. COLI THYMIDYLATE KINASE WITH THE BISUBSTRATE INHIBITOR AZTP5A===


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	==About this Structure==		==About this Structure==
	~~5TMP~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TMP OCA].		[[5tmp]] is a 1 chain structure of [[Thymidylate synthase]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TMP OCA].

			==See Also==
			*[[Thymidylate synthase\|Thymidylate synthase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~9826650~~</ref><references group="xtra"/>		<ref group="xtra">PMID:009826650</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: DTMP kinase]]		[[Category: DTMP kinase]]
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	[[Category: Schlichting, I.]]		[[Category: Schlichting, I.]]
	[[Category: Atp:dtmp phosphotransferase]]		[[Category: Atp:dtmp phosphotransferase]]
			[[Category: Transferase]]
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OCA at 10:28, 16 February 2009

2009-02-16T10:28:46Z

← Older revision		Revision as of 10:28, 16 February 2009
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	==About this Structure==		==About this Structure==
	5TMP is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TMP OCA].		5TMP is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TMP OCA].

	==Reference==		==Reference==
	Structural basis for efficient phosphorylation of 3'-azidothymidine monophosphate by Escherichia coli thymidylate kinase., Lavie A, Ostermann N, Brundiers R, Goody RS, Reinstein J, Konrad M, Schlichting I, Proc Natl Acad Sci U S A. 1998 Nov 24;95(24):14045-50. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/9826650 9826650]~~		<ref group="xtra">PMID:9826650</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	~~[[Category: Single protein]]~~
	[[Category: DTMP kinase]]		[[Category: DTMP kinase]]
	[[Category: Lavie, A.]]		[[Category: Lavie, A.]]
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	[[Category: Atp:dtmp phosphotransferase]]		[[Category: Atp:dtmp phosphotransferase]]

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OCA at 11:12, 3 July 2008

2008-07-03T11:12:02Z

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	~~'''~~COMPLEX OF E. COLI THYMIDYLATE KINASE WITH THE BISUBSTRATE INHIBITOR AZTP5A~~'''~~		===COMPLEX OF E. COLI THYMIDYLATE KINASE WITH THE BISUBSTRATE INHIBITOR AZTP5A===


	~~==Overview==~~		<!--
	The crystal structures of Escherichia coli thymidylate kinase (TmpK) in complex with P1-(5'-adenosyl)-P5-(5'-thymidyl)pentaphosphate and P1-(5'-adenosyl)P5-[5'-(3'-azido-3'-deoxythymidine)] pentaphosphate have been solved to 2.0-A and 2.2-A resolution, ~~respectively. The overall structure of~~ the ~~bacterial TmpK is very similar to that of yeast TmpK. In contrast~~ to the ~~human and yeast TmpKs, which phosphorylate 3'-azido-3'-deoxythymidine 5'-monophosphate~~ (~~AZT-MP)~~ at a 200-fold reduced turnover number (kcat) in comparison to the physiological substrate dTMP, reduction of kcat is only 2-fold for the bacterial enzyme. The different kinetic properties toward AZT-MP between the eukaryotic TmpKs and E. coli TmpK can be rationalized by the different ways in which these enzymes stabilize the presumed transition state and the different manner in which a carboxylic acid side chain in the P loop interacts with the deoxyribose of the monophosphate. Yeast TmpK interacts with the 3'-hydroxyl of dTMP through Asp-14 of the P loop in a bidentate manner: ~~binding of AZT-MP results in a shift of the P loop to accommodate the larger substituent~~. ~~In E~~. ~~coli TmpK~~, ~~the corresponding residue~~ is ~~Glu-12, and it interacts in a side-on fashion with~~ the ~~3'-hydroxyl of dTMP~~. This different mode of interaction between the P loop carboxylic acid with the 3' substituent of the monophosphate deoxyribose allows the accommodation of an azido group in the case of the E. coli enzyme without significant P loop movement. In addition, although the yeast enzyme uses Arg-~~15 (a glycine in E. coli) to stabilize the transition state, E. coli seems to use Arg~~-~~153 from a region termed Lid instead. Thus, the binding of AZT-MP to the yeast TmpK results in the shift of a catalytic residue, which is not the case for the bacterial kinase.~~		The line below this paragraph, {{ABSTRACT_PUBMED_9826650}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 9826650 is the PubMed ID number.
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			{{ABSTRACT_PUBMED_9826650}}

	==About this Structure==		==About this Structure==
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	[[Category: Schlichting, I.]]		[[Category: Schlichting, I.]]
	[[Category: Atp:dtmp phosphotransferase]]		[[Category: Atp:dtmp phosphotransferase]]
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