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4oql

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==Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with dF-EdU==
==Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with dF-EdU==
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<StructureSection load='4oql' size='340' side='right' caption='[[4oql]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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<StructureSection load='4oql' size='340' side='right'caption='[[4oql]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4oql]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OQL FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4oql]] 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=4OQL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OQL FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F2U:2-DEOXY-5-ETHYNYL-2,2-DIFLUOROURIDINE'>F2U</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4oqm|4oqm]], [[4oqn|4oqn]], [[4oqx|4oqx]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F2U:2-DEOXY-5-ETHYNYL-2,2-DIFLUOROURIDINE'>F2U</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4oql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oql OCA], [https://pdbe.org/4oql PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oql RCSB], [https://www.ebi.ac.uk/pdbsum/4oql PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oql ProSAT]</span></td></tr>
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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=4oql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oql OCA], [http://pdbe.org/4oql PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4oql RCSB], [http://www.ebi.ac.uk/pdbsum/4oql PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4oql ProSAT]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[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).
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[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).
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 4oql" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
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*[[Thymidine kinase|Thymidine kinase]]
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*[[Thymidine kinase 3D structures|Thymidine kinase 3D structures]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Thymidine kinase]]
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[[Category: Human alphaherpesvirus 1 strain 17]]
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[[Category: Luedtke, N]]
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[[Category: Large Structures]]
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[[Category: Neef, A B]]
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[[Category: Luedtke N]]
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[[Category: Pernot, L]]
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[[Category: Neef AB]]
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[[Category: Perozzo, R]]
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[[Category: Pernot L]]
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[[Category: Scapozza, L]]
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[[Category: Perozzo R]]
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[[Category: Westermaier, Y]]
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[[Category: Scapozza L]]
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[[Category: 5-ethynyluridine nucleoside derivative]]
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[[Category: Westermaier Y]]
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[[Category: Atp-binding]]
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[[Category: Dna synthesis]]
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[[Category: Nucleotide-binding]]
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[[Category: Transferase]]
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Current revision

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

PDB ID 4oql

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