This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


4oqx

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (17:18, 20 September 2023) (edit) (undo)
 
(4 intermediate revisions not shown.)
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]] 2.50&Aring;' scene=''>
+
<StructureSection load='4oqx' size='340' side='right'caption='[[4oqx]], [[Resolution|resolution]] 2.50&Aring;' 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 [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><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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</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='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><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=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><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 ==
-
<div style="background-color:#fffaf0;">
+
[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).
-
== 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>
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
==See Also==
-
</div>
+
*[[Thymidine kinase 3D structures|Thymidine kinase 3D structures]]
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Thymidine kinase]]
+
[[Category: Human alphaherpesvirus 1 strain 17]]
-
[[Category: Luedtke, N.]]
+
[[Category: Large Structures]]
-
[[Category: Neef, A B.]]
+
[[Category: Luedtke N]]
-
[[Category: Pernot, L.]]
+
[[Category: Neef AB]]
-
[[Category: Perozzo, R.]]
+
[[Category: Pernot L]]
-
[[Category: Scapozza, L.]]
+
[[Category: Perozzo R]]
-
[[Category: Westermaier, Y.]]
+
[[Category: Scapozza L]]
-
[[Category: 5-ethynyluridine nucleoside derivative]]
+
[[Category: Westermaier Y]]
-
[[Category: Atp-binding]]
+
-
[[Category: Dna synthesis]]
+
-
[[Category: Nucleotide-binding]]
+
-
[[Category: Thymidine kinase]]
+
-
[[Category: Transferase]]
+

Current revision

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

PDB ID 4oqx

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4oqx"
Personal tools