5fuv - Revision history

OCA at 13:27, 26 July 2023

OCA — Wed, 26 Jul 2023 13:27:41 GMT

←Older revision		Revision as of 13:27, 26 July 2023
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	<StructureSection load='5fuv' size='340' side='right'caption='[[5fuv]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5fuv' size='340' side='right'caption='[[5fuv]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fuv]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Trypanosoma_(trypanozoon)_brucei~~ Trypanosoma ~~(trypanozoon)~~ brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FUV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5FUV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fuv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_brucei Trypanosoma brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FUV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FUV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</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]] 2.3Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fuw\|5fuw]], [[5fux\|5fux]], [[5fuy\|5fuy]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=5fuv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fuv OCA], [https://pdbe.org/5fuv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fuv RCSB], [https://www.ebi.ac.uk/pdbsum/5fuv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fuv ProSAT]</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=5fuv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fuv OCA], [~~http~~://pdbe.org/5fuv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fuv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fuv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fuv ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q38CF2_TRYB2 Q38CF2_TRYB2]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 21:

	==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: ~~Thymidine kinase~~]]	+	[[Category: Trypanosoma brucei]]
-	[[Category: Balzarini, T]]	+	[[Category: Balzarini T]]
-	[[Category: Castillo-Acosta, V]]	+	[[Category: Castillo-Acosta V]]
-	[[Category: Gonzalez-Pacanowska, D]]	+	[[Category: Gonzalez-Pacanowska D]]
-	[[Category: Nettleship~~, J E~~]]	+	[[Category: Nettleship JE]]
-	[[Category: Rada, H]]	+	[[Category: Rada H]]
-	[[Category: Timm, J]]	+	[[Category: Timm J]]
-	[[Category: Valente, M]]	+	[[Category: Valente M]]
-	[[Category: Wilson~~, K S]]~~	+	[[Category: Wilson KS]]
-	~~[[Category: Dthd]]~~	+
-	~~[[Category: T brucei]]~~	+
-	~~[[Category: Tbtk]]~~	+
-	~~[[Category: Tkii]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:38, 6 May 2020

OCA — Wed, 06 May 2020 07:38:30 GMT

←Older revision		Revision as of 07:38, 6 May 2020
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	==catalytic domain of Thymidine kinase from Trypanosoma brucei with dThd==		==catalytic domain of Thymidine kinase from Trypanosoma brucei with dThd==
-	<StructureSection load='5fuv' size='340' side='right' caption='[[5fuv]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5fuv' size='340' side='right'caption='[[5fuv]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fuv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FUV OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FUV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fuv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_(trypanozoon)_brucei Trypanosoma (trypanozoon) brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FUV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FUV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</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">[[5fuw\|5fuw]], [[5fux\|5fux]], [[5fuy\|5fuy]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fuw\|5fuw]], [[5fux\|5fux]], [[5fuy\|5fuy]]</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=5fuv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fuv OCA], [http://pdbe.org/5fuv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fuv RCSB], [http://www.ebi.ac.uk/pdbsum/5fuv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fuv ProSAT]</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=5fuv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fuv OCA], [http://pdbe.org/5fuv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fuv RCSB], [http://www.ebi.ac.uk/pdbsum/5fuv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fuv ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 25:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Thymidine kinase]]		[[Category: Thymidine kinase]]
	[[Category: Balzarini, T]]		[[Category: Balzarini, T]]

OCA at 20:05, 9 December 2016

OCA — Fri, 09 Dec 2016 20:05:20 GMT

←Older revision		Revision as of 20:05, 9 December 2016
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5fuv" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5fuv" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Thymidine kinase\|Thymidine kinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:39, 27 July 2016

OCA — Wed, 27 Jul 2016 15:39:53 GMT

←Older revision		Revision as of 15:39, 27 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5fuv is ~~ON HOLD until Paper~~ Publication	+	==catalytic domain of Thymidine kinase from Trypanosoma brucei with dThd==
		+	<StructureSection load='5fuv' size='340' side='right' caption='[[5fuv]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5fuv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FUV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FUV FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</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">[[5fuw\|5fuw]], [[5fux\|5fux]], [[5fuy\|5fuy]]</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=5fuv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fuv OCA], [http://pdbe.org/5fuv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fuv RCSB], [http://www.ebi.ac.uk/pdbsum/5fuv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fuv ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Thymidine kinase (TK) is a key enzyme in the pyrimidine salvage pathway which catalyzes the transfer of the gamma-phosphate of ATP to 2'-deoxythymidine (dThd) forming thymidine monophosphate (dTMP). Unlike other type II TKs, the Trypanosoma brucei enzyme (TbTK) is a tandem protein with two TK homolog domains of which only the C-terminal one is active. In this study, we establish that TbTK is essential for parasite viability and cell cycle progression, independently of extracellular pyrimidine concentrations. We show that expression of TbTK is cell cycle regulated and that depletion of TbTK leads to strongly diminished dTTP pools and DNA damage indicating intracellular dThd to be an essential intermediate metabolite for the synthesis of thymine-derived nucleotides. In addition, we report the X-ray structure of the catalytically active domain of TbTK in complex with dThd and dTMP at resolutions up to 2.2 A. In spite of the high conservation of the active site residues, the structures reveal a widened active site cavity near the nucleobase moiety compared to the human enzyme. Our findings strongly support TbTK as a crucial enzyme in dTTP homeostasis and identify structural differences within the active site that could be exploited in the process of rational drug design. This article is protected by copyright. All rights reserved.

-	~~Authors: Timm~~, J., Valente, M., Castillo-Acosta, V., Balzarini, T., Nettleship, ~~J.E.~~, Rada, H., Wilson~~, K.S.~~, Gonzalez-Pacanowska, D.	+	Cell cycle regulation and novel structural features of thymidine kinase, an essential enzyme in Trypanosoma brucei.,Valente M, Timm J, Castillo-Acosta VM, Ruiz-Perez LM, Balzarini T, Nettleship JE, Bird LE, Rada H, Wilson KS, Gonzalez-Pacanowska D Mol Microbiol. 2016 Jul 18. doi: 10.1111/mmi.13467. PMID:27426054<ref>PMID:27426054</ref>

-	~~Description: catalytic domain~~ of ~~Thymidine kinase from Trypanosoma brucei with dThd~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category: Wilson, K~~.S]]	+	<div class="pdbe-citations 5fuv" style="background-color:#fffaf0;"></div>
-	~~[[Category~~: ~~Rada, H]]~~	+	== References ==
-	[[Category: ~~Nettleship, J.E~~]]	+	<references/>
-	[[Category: ~~Gonzalez-Pacanowska~~, D]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Thymidine kinase]]
		+	[[Category: Balzarini, T]]
	[[Category: Castillo-Acosta, V]]		[[Category: Castillo-Acosta, V]]
-	[[Category: ~~Valente~~, M]]	+	[[Category: Gonzalez-Pacanowska, D]]
		+	[[Category: Nettleship, J E]]
		+	[[Category: Rada, H]]
	[[Category: Timm, J]]		[[Category: Timm, J]]
-	[[Category: ~~Balzarini~~, T]]	+	[[Category: Valente, M]]
		+	[[Category: Wilson, K S]]
		+	[[Category: Dthd]]
		+	[[Category: T brucei]]
		+	[[Category: Tbtk]]
		+	[[Category: Tkii]]
		+	[[Category: Transferase]]

OCA at 00:25, 21 February 2016

OCA — Sun, 21 Feb 2016 00:25:24 GMT

←Older revision		Revision as of 00:25, 21 February 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5fuv is ON HOLD	+	The entry 5fuv is ON HOLD until Paper Publication

	Authors: Timm, J., Valente, M., Castillo-Acosta, V., Balzarini, T., Nettleship, J.E., Rada, H., Wilson, K.S., Gonzalez-Pacanowska, D.		Authors: Timm, J., Valente, M., Castillo-Acosta, V., Balzarini, T., Nettleship, J.E., Rada, H., Wilson, K.S., Gonzalez-Pacanowska, D.

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

OCA — Wed, 10 Feb 2016 14:56:35 GMT

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

←Older revision

Revision as of 14:56, 10 February 2016

OCA: New page: '''Unreleased structure''' The entry 5fuv is ON HOLD Authors: Timm, J., Valente, M., Castillo-Acosta, V., Balzarini, T., Nettleship, J.E., Rada, H., Wilson, K.S., Gonzalez-Pacanowska, D...

OCA — Wed, 10 Feb 2016 14:56:33 GMT

New page: '''Unreleased structure''' The entry 5fuv is ON HOLD Authors: Timm, J., Valente, M., Castillo-Acosta, V., Balzarini, T., Nettleship, J.E., Rada, H., Wilson, K.S., Gonzalez-Pacanowska, D...

New page

'''Unreleased structure'''

The entry 5fuv is ON HOLD

Authors: Timm, J., Valente, M., Castillo-Acosta, V., Balzarini, T., Nettleship, J.E., Rada, H., Wilson, K.S., Gonzalez-Pacanowska, D.

Description: catalytic domain of Thymidine kinase from Trypanosoma brucei with dThd
[[Category: Unreleased Structures]]
[[Category: Wilson, K.S]]
[[Category: Rada, H]]
[[Category: Nettleship, J.E]]
[[Category: Gonzalez-Pacanowska, D]]
[[Category: Castillo-Acosta, V]]
[[Category: Valente, M]]
[[Category: Timm, J]]
[[Category: Balzarini, T]]