4uxj - Revision history

OCA at 11:24, 9 May 2024

OCA — Thu, 09 May 2024 11:24:21 GMT

←Older revision		Revision as of 11:24, 9 May 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4uxj]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Leishmania_major Leishmania major]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UXJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UXJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4uxj]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Leishmania_major Leishmania major]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UXJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UXJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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]] 3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=4uxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uxj OCA], [https://pdbe.org/4uxj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4uxj RCSB], [https://www.ebi.ac.uk/pdbsum/4uxj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4uxj 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=4uxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uxj OCA], [https://pdbe.org/4uxj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4uxj RCSB], [https://www.ebi.ac.uk/pdbsum/4uxj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4uxj ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:49, 29 March 2023

OCA — Wed, 29 Mar 2023 07:49:29 GMT

←Older revision		Revision as of 07:49, 29 March 2023
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	<StructureSection load='4uxj' size='340' side='right'caption='[[4uxj]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='4uxj' size='340' side='right'caption='[[4uxj]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4uxj]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Leima Leima~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UXJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4UXJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4uxj]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Leishmania_major Leishmania major]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UXJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UXJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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">[[4uxh\|4uxh]], [[4uxi\|4uxi]]</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=4uxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uxj OCA], [https://pdbe.org/4uxj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4uxj RCSB], [https://www.ebi.ac.uk/pdbsum/4uxj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4uxj ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/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=4uxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uxj OCA], [~~http~~://pdbe.org/4uxj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4uxj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4uxj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4uxj ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q4QC75_LEIMA Q4QC75_LEIMA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 20:

	==See Also==		==See Also==
-	*[[Thymidine kinase\|Thymidine kinase]]	+	*[[Thymidine kinase 3D structures\|Thymidine kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Leima]]~~	+	[[Category: Leishmania major]]
-	~~[[Category: Thymidine kinase~~]]	+	[[Category: Bosch-Navarrete C]]
-	[[Category: Bosch-Navarrete, C]]	+	[[Category: Gonzalez-Pacanowska D]]
-	[[Category: Gonzalez-Pacanowska, D]]	+	[[Category: Nettleship JE]]
-	[[Category: Nettleship~~, J E~~]]	+	[[Category: Rada H]]
-	[[Category: Rada, H]]	+	[[Category: Recio E]]
-	[[Category: Recio, E]]	+	[[Category: Timm J]]
-	[[Category: Timm, J]]	+	[[Category: Wilson KS]]
-	[[Category: Wilson~~, K S]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:09, 23 May 2019

OCA — Thu, 23 May 2019 08:09:48 GMT

←Older revision		Revision as of 08:09, 23 May 2019
Line 1:		Line 1:

	==Leishmania major Thymidine Kinase in complex with dTTP==		==Leishmania major Thymidine Kinase in complex with dTTP==
-	<StructureSection load='4uxj' size='340' side='right' caption='[[4uxj]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='4uxj' size='340' side='right'caption='[[4uxj]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4uxj]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UXJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UXJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4uxj]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Leima Leima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UXJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UXJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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">[[4uxh\|4uxh]], [[4uxi\|4uxi]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4uxh\|4uxh]], [[4uxi\|4uxi]]</td></tr>
Line 25:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Leima]]
	[[Category: Thymidine kinase]]		[[Category: Thymidine kinase]]
	[[Category: Bosch-Navarrete, C]]		[[Category: Bosch-Navarrete, C]]

OCA at 01:52, 10 March 2017

OCA — Fri, 10 Mar 2017 01:52:56 GMT

←Older revision		Revision as of 01:52, 10 March 2017
Line 1:		Line 1:
		+
	==Leishmania major Thymidine Kinase in complex with dTTP==		==Leishmania major Thymidine Kinase in complex with dTTP==
	<StructureSection load='4uxj' size='340' side='right' caption='[[4uxj]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='4uxj' size='340' side='right' caption='[[4uxj]], [[Resolution\|resolution]] 3.00Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4uxh\|4uxh]], [[4uxi\|4uxi]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4uxh\|4uxh]], [[4uxi\|4uxi]]</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=4uxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uxj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4uxj RCSB], [http://www.ebi.ac.uk/pdbsum/4uxj 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=4uxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uxj OCA], [http://pdbe.org/4uxj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4uxj RCSB], [http://www.ebi.ac.uk/pdbsum/4uxj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4uxj ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 4uxj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Thymidine kinase\|Thymidine kinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:55, 27 May 2015

OCA — Wed, 27 May 2015 15:55:13 GMT

←Older revision		Revision as of 15:55, 27 May 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Leishmania major Thymidine Kinase in complex with dTTP==
		+	<StructureSection load='4uxj' size='340' side='right' caption='[[4uxj]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4uxj]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UXJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UXJ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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">[[4uxh\|4uxh]], [[4uxi\|4uxi]]</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=4uxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uxj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4uxj RCSB], [http://www.ebi.ac.uk/pdbsum/4uxj PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Leishmania spp. is a protozoan parasite and the causative agent of leishmaniasis. Thymidine kinase (TK) catalyses the transfer of the gamma-phosphate of ATP to 2'-deoxythymidine (dThd) forming thymidine monophosphate (dTMP). L. major Type II TK (LmTK) has been previously shown to be important for infectivity of the parasite and therefore has potential as a drug target for anti-leishmanial therapy. In this study, we determined the enzymatic properties and the 3D structures of holo forms of the enzyme. LmTK efficiently phosphorylates dThd and dUrd and has high structural homology to TKs from other species. However, it significantly differs in its kinetic properties from Trypanosoma brucei TK since purines are not substrates of the enzyme and dNTPs such as dUTP inhibit LmTK. The enzyme had Km and kcat values for dThd of 1.1 muM and 2.62 s-1 and exhibits cooperative binding for ATP. Additionally, we show that the anti-retroviral prodrug zidovudine (3-azido-3-deoxythymidine, AZT) and 5'-modified dUrd can be readily phosphorylated by LmTK. The production of recombinant enzyme at a level suitable for structural studies was achieved by the construction of C-terminal truncated versions of the enzyme and the use of a baculoviral expression system. The structures of the catalytic core of LmTK in complex with dThd, the negative feedback regulator dTTP and the bi-substrate analogue AP5dT, were determined to 2.74, 3.00 and 2.40 A, respectively, and provide the structural basis for exclusion of purines and dNTP inhibition. The results will aid the process of rational drug design with LmTK as a potential target for anti-leishmanial drugs.

-	~~The entry 4uxj is ON HOLD until Paper Publication~~	+	Structural and Kinetic Characterization of Thymidine Kinase from Leishmania major.,Timm J, Bosch-Navarrete C, Recio E, Nettleship JE, Rada H, Gonzalez-Pacanowska D, Wilson KS PLoS Negl Trop Dis. 2015 May 15;9(5):e0003781. doi: 10.1371/journal.pntd.0003781., eCollection 2015 May. PMID:25978379<ref>PMID:25978379</ref>

-	~~Authors: Timm~~, J.~~, Bosch-Navarrete, C~~.~~, Recio, E., Nettleship, J.E., Rada, H., Gonzalez-Pacanowska, D., Wilson, K.S~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Leishmania major Thymidine Kinase in complex with dTTP~~	+	== References ==
-	~~[[Category: Unreleased Structures]]~~	+	<references/>
-	~~[[Category: Wilson, K.S]]~~	+	__TOC__
-	~~[[Category: Rada, H]]~~	+	</StructureSection>
-	[[Category: ~~Nettleship, J.E~~]]	+	[[Category: Thymidine kinase]]
	[[Category: Bosch-Navarrete, C]]		[[Category: Bosch-Navarrete, C]]
	[[Category: Gonzalez-Pacanowska, D]]		[[Category: Gonzalez-Pacanowska, D]]
		+	[[Category: Nettleship, J E]]
		+	[[Category: Rada, H]]
	[[Category: Recio, E]]		[[Category: Recio, E]]
	[[Category: Timm, J]]		[[Category: Timm, J]]
		+	[[Category: Wilson, K S]]
		+	[[Category: Transferase]]

OCA at 18:51, 24 December 2014

OCA — Wed, 24 Dec 2014 18:51:38 GMT

←Older revision		Revision as of 18:51, 24 December 2014
Line 6:		Line 6:

	Description: Leishmania major Thymidine Kinase in complex with dTTP		Description: Leishmania major Thymidine Kinase in complex with dTTP
		+	[[Category: Unreleased Structures]]
		+	[[Category: Wilson, K.S]]
		+	[[Category: Rada, H]]
		+	[[Category: Nettleship, J.E]]
		+	[[Category: Bosch-Navarrete, C]]
		+	[[Category: Gonzalez-Pacanowska, D]]
		+	[[Category: Recio, E]]
		+	[[Category: Timm, J]]

OCA at 08:45, 10 September 2014

OCA — Wed, 10 Sep 2014 08:45:14 GMT

←Older revision		Revision as of 08:45, 10 September 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4uxj is ON HOLD until ~~sometime in the future~~	+	The entry 4uxj is ON HOLD until Paper Publication

	Authors: Timm, J., Bosch-Navarrete, C., Recio, E., Nettleship, J.E., Rada, H., Gonzalez-Pacanowska, D., Wilson, K.S.		Authors: Timm, J., Bosch-Navarrete, C., Recio, E., Nettleship, J.E., Rada, H., Gonzalez-Pacanowska, D., Wilson, K.S.

	Description: Leishmania major Thymidine Kinase in complex with dTTP		Description: Leishmania major Thymidine Kinase in complex with dTTP

OCA: Protected "4uxj" [edit=sysop:move=sysop]

OCA — Thu, 04 Sep 2014 04:41:13 GMT

Protected "4uxj" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:41, 4 September 2014

OCA: New page: '''Unreleased structure''' The entry 4uxj is ON HOLD until sometime in the future Authors: Timm, J., Bosch-Navarrete, C., Recio, E., Nettleship, J.E., Rada, H., Gonzalez-Pacanowska, D.,...

OCA — Thu, 04 Sep 2014 04:41:12 GMT

New page: '''Unreleased structure''' The entry 4uxj is ON HOLD until sometime in the future Authors: Timm, J., Bosch-Navarrete, C., Recio, E., Nettleship, J.E., Rada, H., Gonzalez-Pacanowska, D.,...

New page

'''Unreleased structure'''

The entry 4uxj is ON HOLD until sometime in the future

Authors: Timm, J., Bosch-Navarrete, C., Recio, E., Nettleship, J.E., Rada, H., Gonzalez-Pacanowska, D., Wilson, K.S.

Description: Leishmania major Thymidine Kinase in complex with dTTP