4oqx - Revision history

OCA at 17:18, 20 September 2023

OCA — Wed, 20 Sep 2023 17:18:07 GMT

←Older revision		Revision as of 17:18, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4oqx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_alphaherpesvirus_1_strain_17 Human alphaherpesvirus 1 strain 17]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OQX FirstGlance]. <br>		<table><tr><td colspan='2'>[[4oqx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_alphaherpesvirus_1_strain_17 Human alphaherpesvirus 1 strain 17]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OQX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDV:1-(2-DEOXY-2-METHYL-BETA-D-ARABINOFURANOSYL)-5-ETHYNYLPYRIMIDINE-2,4(1H,3H)-DIONE'>EDV</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.5Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDV:1-(2-DEOXY-2-METHYL-BETA-D-ARABINOFURANOSYL)-5-ETHYNYLPYRIMIDINE-2,4(1H,3H)-DIONE'>EDV</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4oqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqx OCA], [https://pdbe.org/4oqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oqx RCSB], [https://www.ebi.ac.uk/pdbsum/4oqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oqx 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=4oqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqx OCA], [https://pdbe.org/4oqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oqx RCSB], [https://www.ebi.ac.uk/pdbsum/4oqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oqx ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:41, 25 January 2023

OCA — Wed, 25 Jan 2023 07:41:03 GMT

←Older revision		Revision as of 07:41, 25 January 2023
Line 1:		Line 1:

	==Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with Me-ARA-EdU==		==Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with Me-ARA-EdU==
-	<StructureSection load='4oqx' size='340' side='right' caption='[[4oqx]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='4oqx' size='340' side='right'caption='[[4oqx]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4oqx]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Hhv-1 Hhv-~~1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4OQX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4oqx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_alphaherpesvirus_1_strain_17 Human alphaherpesvirus 1 strain 17]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OQX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDV:1-(2-DEOXY-2-METHYL-BETA-D-ARABINOFURANOSYL)-5-ETHYNYLPYRIMIDINE-2,4(1H,3H)-DIONE'>EDV</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDV:1-(2-DEOXY-2-METHYL-BETA-D-ARABINOFURANOSYL)-5-ETHYNYLPYRIMIDINE-2,4(1H,3H)-DIONE'>EDV</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oql\|4oql]], [[4oqm\|4oqm]], [[4oqn\|4oqn]]</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=4oqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqx OCA], [https://pdbe.org/4oqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oqx RCSB], [https://www.ebi.ac.uk/pdbsum/4oqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oqx ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TK, TK (UL23), UL23 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10299 HHV-1])</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=4oqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqx OCA], [~~http~~://pdbe.org/4oqx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4oqx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4oqx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4oqx ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/KITH_HHV11 KITH_HHV11]] In latent infection, may allow the virus to be reactivated and to grow in cells lacking a high concentration of phosphorylated nucleic acid precursors, such as nerve cells that do not replicate their genome (By similarity).	+	[https://www.uniprot.org/uniprot/KITH_HHV11 KITH_HHV11] In latent infection, may allow the virus to be reactivated and to grow in cells lacking a high concentration of phosphorylated nucleic acid precursors, such as nerve cells that do not replicate their genome (By similarity).
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Commonly used metabolic labels for DNA, including 5-ethynyl-2'-deoxyuridine (EdU) and BrdU, are toxic antimetabolites that cause DNA instability, necrosis, and cell-cycle arrest. In addition to perturbing biological function, these properties can prevent metabolic labeling studies where subsequent tissue survival is needed. To bypass the metabolic pathways responsible for toxicity, while maintaining the ability to be metabolically incorporated into DNA, we synthesized and evaluated a small family of arabinofuranosyl-ethynyluracil derivatives. Among these, (2'S)-2'-deoxy-2'-fluoro-5-ethynyluridine (F-ara-EdU) exhibited selective DNA labeling, yet had a minimal impact on genome function in diverse tissue types. Metabolic incorporation of F-ara-EdU into DNA was readily detectable using copper(I)-catalyzed azide-alkyne "click" reactions with fluorescent azides. F-ara-EdU is less toxic than both BrdU and EdU, and it can be detected with greater sensitivity in experiments where long-term cell survival and/or deep-tissue imaging are desired. In contrast to previously reported 2'-arabino modified nucleosides and EdU, F-ara-EdU causes little or no cellular arrest or DNA synthesis inhibition. F-ara-EdU is therefore ideally suited for pulse-chase experiments aimed at "birth dating" DNA in vivo. As a demonstration, Zebrafish embryos were microinjected with F-ara-EdU at the one-cell stage and chased by BrdU at 10 h after fertilization. Following 3 d of development, complex patterns of quiescent/senescent cells containing only F-ara-EdU were observed in larvae along the dorsal side of the notochord and epithelia. Arabinosyl nucleoside derivatives therefore provide unique and effective means to introduce bioorthogonal functional groups into DNA for diverse applications in basic research, biotechnology, and drug discovery.	+

-	Dynamic metabolic labeling of DNA in vivo with arabinosyl nucleosides.,Neef AB, Luedtke NW Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20404-9. doi:, 10.1073/pnas.1101126108. Epub 2011 Dec 5. PMID:22143759<ref>PMID:22143759</ref>	+	==See Also==
-		+	*[[Thymidine kinase 3D structures\|Thymidine kinase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 4oqx" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Hhv-~~1]]	+	[[Category: Human alphaherpesvirus 1 strain 17]]
-	[[Category: ~~Thymidine kinase~~]]	+	[[Category: Large Structures]]
-	[[Category: Luedtke, N]]	+	[[Category: Luedtke N]]
-	[[Category: Neef~~, A B~~]]	+	[[Category: Neef AB]]
-	[[Category: Pernot, L]]	+	[[Category: Pernot L]]
-	[[Category: Perozzo, R]]	+	[[Category: Perozzo R]]
-	[[Category: Scapozza, L]]	+	[[Category: Scapozza L]]
-	[[Category: Westermaier, Y]]	+	[[Category: Westermaier Y]]
-	~~[[Category: 5-ethynyluridine nucleoside derivative]]~~	+
-	~~[[Category: Atp-binding]]~~	+
-	~~[[Category: Dna synthesis]]~~	+
-	~~[[Category: Nucleotide-binding]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:29, 22 November 2017

OCA — Wed, 22 Nov 2017 08:29:09 GMT

←Older revision		Revision as of 08:29, 22 November 2017
Line 3:		Line 3:
	<StructureSection load='4oqx' size='340' side='right' caption='[[4oqx]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='4oqx' size='340' side='right' caption='[[4oqx]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4oqx]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OQX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4oqx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Hhv-1 Hhv-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OQX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDV:1-(2-DEOXY-2-METHYL-BETA-D-ARABINOFURANOSYL)-5-ETHYNYLPYRIMIDINE-2,4(1H,3H)-DIONE'>EDV</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDV:1-(2-DEOXY-2-METHYL-BETA-D-ARABINOFURANOSYL)-5-ETHYNYLPYRIMIDINE-2,4(1H,3H)-DIONE'>EDV</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oql\|4oql]], [[4oqm\|4oqm]], [[4oqn\|4oqn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oql\|4oql]], [[4oqm\|4oqm]], [[4oqn\|4oqn]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TK, TK (UL23), UL23 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10299 HHV-1])</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=4oqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqx OCA], [http://pdbe.org/4oqx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4oqx RCSB], [http://www.ebi.ac.uk/pdbsum/4oqx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4oqx ProSAT]</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=4oqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqx OCA], [http://pdbe.org/4oqx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4oqx RCSB], [http://www.ebi.ac.uk/pdbsum/4oqx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4oqx ProSAT]</span></td></tr>
Line 20:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 4oqx" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4oqx" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Thymidine kinase\|Thymidine kinase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Hhv-1]]
	[[Category: Thymidine kinase]]		[[Category: Thymidine kinase]]
	[[Category: Luedtke, N]]		[[Category: Luedtke, N]]

OCA at 13:07, 5 August 2016

OCA — Fri, 05 Aug 2016 13:07:10 GMT

←Older revision		Revision as of 13:07, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with Me-ARA-EdU==		==Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with Me-ARA-EdU==
	<StructureSection load='4oqx' size='340' side='right' caption='[[4oqx]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='4oqx' size='340' side='right' caption='[[4oqx]], [[Resolution\|resolution]] 2.50Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oql\|4oql]], [[4oqm\|4oqm]], [[4oqn\|4oqn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oql\|4oql]], [[4oqm\|4oqm]], [[4oqn\|4oqn]]</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=4oqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oqx RCSB], [http://www.ebi.ac.uk/pdbsum/4oqx 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=4oqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqx OCA], [http://pdbe.org/4oqx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4oqx RCSB], [http://www.ebi.ac.uk/pdbsum/4oqx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4oqx ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 4oqx" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Thymidine kinase\|Thymidine kinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 02:43, 25 December 2014

OCA — Thu, 25 Dec 2014 02:43:16 GMT

←Older revision		Revision as of 02:43, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4oqx]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OQX FirstGlance]. <br>		<table><tr><td colspan='2'>[[4oqx]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OQX FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDV:1-(2-DEOXY-2-METHYL-BETA-D-ARABINOFURANOSYL)-5-ETHYNYLPYRIMIDINE-2,4(1H,3H)-DIONE'>EDV</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDV:1-(2-DEOXY-2-METHYL-BETA-D-ARABINOFURANOSYL)-5-ETHYNYLPYRIMIDINE-2,4(1H,3H)-DIONE'>EDV</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oql\|4oql]], [[4oqm\|4oqm]], [[4oqn\|4oqn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oql\|4oql]], [[4oqm\|4oqm]], [[4oqn\|4oqn]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidine_kinase Thymidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.21 2.7.1.21] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidine_kinase Thymidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.21 2.7.1.21] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4oqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oqx RCSB], [http://www.ebi.ac.uk/pdbsum/4oqx 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=4oqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oqx RCSB], [http://www.ebi.ac.uk/pdbsum/4oqx PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KITH_HHV11 KITH_HHV11]] In latent infection, may allow the virus to be reactivated and to grow in cells lacking a high concentration of phosphorylated nucleic acid precursors, such as nerve cells that do not replicate their genome (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Thymidine kinase]]		[[Category: Thymidine kinase]]
-	[[Category: Luedtke, N.]]	+	[[Category: Luedtke, N]]
-	[[Category: Neef, A B.]]	+	[[Category: Neef, A B]]
-	[[Category: Pernot, L.]]	+	[[Category: Pernot, L]]
-	[[Category: Perozzo, R.]]	+	[[Category: Perozzo, R]]
-	[[Category: Scapozza, L.]]	+	[[Category: Scapozza, L]]
-	[[Category: Westermaier, Y.]]	+	[[Category: Westermaier, Y]]
	[[Category: 5-ethynyluridine nucleoside derivative]]		[[Category: 5-ethynyluridine nucleoside derivative]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Dna synthesis]]		[[Category: Dna synthesis]]
	[[Category: Nucleotide-binding]]		[[Category: Nucleotide-binding]]
-	[[Category: Thymidine kinase]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 09:04, 13 August 2014

OCA — Wed, 13 Aug 2014 09:04:54 GMT

←Older revision		Revision as of 09:04, 13 August 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with Me-ARA-EdU==
		+	<StructureSection load='4oqx' size='340' side='right' caption='[[4oqx]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4oqx]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OQX FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDV:1-(2-DEOXY-2-METHYL-BETA-D-ARABINOFURANOSYL)-5-ETHYNYLPYRIMIDINE-2,4(1H,3H)-DIONE'>EDV</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oql\|4oql]], [[4oqm\|4oqm]], [[4oqn\|4oqn]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidine_kinase Thymidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.21 2.7.1.21] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4oqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oqx RCSB], [http://www.ebi.ac.uk/pdbsum/4oqx PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Commonly used metabolic labels for DNA, including 5-ethynyl-2'-deoxyuridine (EdU) and BrdU, are toxic antimetabolites that cause DNA instability, necrosis, and cell-cycle arrest. In addition to perturbing biological function, these properties can prevent metabolic labeling studies where subsequent tissue survival is needed. To bypass the metabolic pathways responsible for toxicity, while maintaining the ability to be metabolically incorporated into DNA, we synthesized and evaluated a small family of arabinofuranosyl-ethynyluracil derivatives. Among these, (2'S)-2'-deoxy-2'-fluoro-5-ethynyluridine (F-ara-EdU) exhibited selective DNA labeling, yet had a minimal impact on genome function in diverse tissue types. Metabolic incorporation of F-ara-EdU into DNA was readily detectable using copper(I)-catalyzed azide-alkyne "click" reactions with fluorescent azides. F-ara-EdU is less toxic than both BrdU and EdU, and it can be detected with greater sensitivity in experiments where long-term cell survival and/or deep-tissue imaging are desired. In contrast to previously reported 2'-arabino modified nucleosides and EdU, F-ara-EdU causes little or no cellular arrest or DNA synthesis inhibition. F-ara-EdU is therefore ideally suited for pulse-chase experiments aimed at "birth dating" DNA in vivo. As a demonstration, Zebrafish embryos were microinjected with F-ara-EdU at the one-cell stage and chased by BrdU at 10 h after fertilization. Following 3 d of development, complex patterns of quiescent/senescent cells containing only F-ara-EdU were observed in larvae along the dorsal side of the notochord and epithelia. Arabinosyl nucleoside derivatives therefore provide unique and effective means to introduce bioorthogonal functional groups into DNA for diverse applications in basic research, biotechnology, and drug discovery.

-	~~The entry 4oqx is ON HOLD until Aug~~ 10 ~~2015~~	+	Dynamic metabolic labeling of DNA in vivo with arabinosyl nucleosides.,Neef AB, Luedtke NW Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20404-9. doi:, 10.1073/pnas.1101126108. Epub 2011 Dec 5. PMID:22143759<ref>PMID:22143759</ref>

-	~~Authors: Pernot~~, L., Neef, A.B., ~~Westermaier, Y~~., Perozzo, R.~~, Luedtke, N.,~~ Scapozza, L.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with Me~~-~~ARA~~-~~EdU~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Thymidine kinase]]
		+	[[Category: Luedtke, N.]]
		+	[[Category: Neef, A B.]]
		+	[[Category: Pernot, L.]]
		+	[[Category: Perozzo, R.]]
		+	[[Category: Scapozza, L.]]
		+	[[Category: Westermaier, Y.]]
		+	[[Category: 5-ethynyluridine nucleoside derivative]]
		+	[[Category: Atp-binding]]
		+	[[Category: Dna synthesis]]
		+	[[Category: Nucleotide-binding]]
		+	[[Category: Thymidine kinase]]
		+	[[Category: Transferase]]

OCA at 16:49, 3 March 2014

OCA — Mon, 03 Mar 2014 16:49:23 GMT

←Older revision		Revision as of 16:49, 3 March 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4oqx is ON HOLD	+	The entry 4oqx is ON HOLD until Aug 10 2015

	Authors: Pernot, L., Neef, A.B., Westermaier, Y., Perozzo, R., Luedtke, N., Scapozza, L.		Authors: Pernot, L., Neef, A.B., Westermaier, Y., Perozzo, R., Luedtke, N., Scapozza, L.

-	Description: Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with Me-EdU	+	Description: Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with Me-ARA-EdU

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

OCA — Wed, 19 Feb 2014 16:20:05 GMT

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

←Older revision

Revision as of 16:20, 19 February 2014

OCA: New page: '''Unreleased structure''' The entry 4oqx is ON HOLD Authors: Pernot, L., Neef, A.B., Westermaier, Y., Perozzo, R., Luedtke, N., Scapozza, L. Description: Crystal structure of thymidin...

OCA — Wed, 19 Feb 2014 16:20:04 GMT

New page: '''Unreleased structure''' The entry 4oqx is ON HOLD Authors: Pernot, L., Neef, A.B., Westermaier, Y., Perozzo, R., Luedtke, N., Scapozza, L. Description: Crystal structure of thymidin...

New page

'''Unreleased structure'''

The entry 4oqx is ON HOLD

Authors: Pernot, L., Neef, A.B., Westermaier, Y., Perozzo, R., Luedtke, N., Scapozza, L.

Description: Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with Me-EdU