4jby

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:39, 20 September 2023) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
 +
==Crystal structure of thymidine kinase from Herpes simplex virus type 1 in complex with F-SK78==
==Crystal structure of thymidine kinase from Herpes simplex virus type 1 in complex with F-SK78==
-
<StructureSection load='4jby' size='340' side='right' caption='[[4jby]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+
<StructureSection load='4jby' size='340' side='right'caption='[[4jby]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4jby]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Herpes_simplex_virus_(type_1_/_strain_17) Herpes simplex virus (type 1 / strain 17)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JBY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JBY FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4jby]] 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=4JBY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JBY FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FSK:6-[(1Z)-3-FLUORO-2-(HYDROXYMETHYL)PROP-1-EN-1-YL]-1,5-DIMETHYLPYRIMIDINE-2,4(1H,3H)-DIONE'>FSK</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&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3f0t|3f0t]], [[3rdp|3rdp]], [[1e2p|1e2p]], [[4ivp|4ivp]], [[4ivq|4ivq]], [[4ivr|4ivr]], [[4jbx|4jbx]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FSK:6-[(1Z)-3-FLUORO-2-(HYDROXYMETHYL)PROP-1-EN-1-YL]-1,5-DIMETHYLPYRIMIDINE-2,4(1H,3H)-DIONE'>FSK</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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 Herpes simplex virus (type 1 / strain 17)])</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=4jby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jby OCA], [https://pdbe.org/4jby PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jby RCSB], [https://www.ebi.ac.uk/pdbsum/4jby PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jby ProSAT]</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=4jby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jby OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jby RCSB], [http://www.ebi.ac.uk/pdbsum/4jby PDBsum]</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 ==
+
-
Novel C-6 substituted pyrimidine derivatives are good substrates of herpes simplex virus type 1 thymidine kinase (HSV1-TK). Enzyme kinetic experiments showed that our lead compound, N-methyl DHBT (N-methyl-6-(1,3-dihydroxyisobutyl) thymine; N-Me DHBT), is phosphorylated at a similar rate compared to "gold standard" 9-[4-fluoro-3-(hydroxymethyl)butyl]guanine, FHBG, (K(m) = 10 +/- 0.3 muM; k(cat) = 0.036 +/- 0.015 sec(-1)). Additionally, it does not show cytotoxic properties on B16F1 cells up to a concentration of 10 mM. The x-ray analysis of the crystal structures of HSV1-TK with N-Me DHBT and of HSV1-TK with the fluorinated derivative N-Me FHBT confirmed the binding mode predicted by docking studies and their substrate characteristics. Moreover, the crystal structure of HSV1-TK with N-Me DHBT revealed an additional water-mediated H-bond interesting for the design of further analogues.
+
-
 
+
-
Synthesis, crystal structure, and in vitro biological evaluation of C-6 pyrimidine derivatives: new lead structures for monitoring gene expression in vivo.,Martic M, Pernot L, Westermaier Y, Perozzo R, Kraljevic TG, Kristafor S, Raic-Malic S, Scapozza L, Ametamey S Nucleosides Nucleotides Nucleic Acids. 2011 Apr;30(4):293-315. PMID:21623543<ref>PMID:21623543</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
==See Also==
==See Also==
-
*[[Thymidine kinase|Thymidine kinase]]
+
*[[Thymidine kinase 3D structures|Thymidine kinase 3D structures]]
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Thymidine kinase]]
+
[[Category: Human alphaherpesvirus 1 strain 17]]
-
[[Category: Novakovic, I]]
+
[[Category: Large Structures]]
-
[[Category: Pernot, L]]
+
[[Category: Novakovic I]]
-
[[Category: Perozzo, R]]
+
[[Category: Pernot L]]
-
[[Category: Raic-Malic, S]]
+
[[Category: Perozzo R]]
-
[[Category: Scapozza, L]]
+
[[Category: Raic-Malic S]]
-
[[Category: Westermaier, Y]]
+
[[Category: Scapozza L]]
-
[[Category: Atp binding]]
+
[[Category: Westermaier Y]]
-
[[Category: Dna synthesis]]
+
-
[[Category: Nucleotide binding]]
+
-
[[Category: Pet imaging tracer]]
+
-
[[Category: Transferase]]
+

Current revision

Crystal structure of thymidine kinase from Herpes simplex virus type 1 in complex with F-SK78

PDB ID 4jby

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/4jby"
Personal tools