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4oqm

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Revision as of 17:47, 4 August 2016

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

Structural highlights

4oqm is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	4oql, 4oqn, 4oqx
Activity:	Thymidine kinase, with EC number 2.7.1.21
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Neef AB, Luedtke NW. Dynamic metabolic labeling of DNA in vivo with arabinosyl nucleosides. 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 doi:http://dx.doi.org/10.1073/pnas.1101126108

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4oqm"

@@ Line 1: / Line 1: @@
 ==Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with F-ARA-EdU==
 <StructureSection load='4oqm' size='340' side='right' caption='[[4oqm]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4oql|4oql]], [[4oqn|4oqn]], [[4oqx|4oqx]]</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=4oqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oqm RCSB], [http://www.ebi.ac.uk/pdbsum/4oqm 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=4oqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqm OCA], [http://pdbe.org/4oqm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4oqm RCSB], [http://www.ebi.ac.uk/pdbsum/4oqm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4oqm ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 18: / Line 19: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4oqm" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Thymidine kinase|Thymidine kinase]]
 == References ==
 <references/>

4oqm

From Proteopedia

Revision as of 17:47, 4 August 2016

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

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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