3vtk: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:3vtk.gif|left|200px]]<br /><applet load="3vtk" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="3vtk, resolution 3.0&Aring;" />
-'''THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH ADP AND 5-IODO-DEOXYURIDINE-MONOPHOSPHATE'''<br />
-==Overview==
+==THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH ADP AND 5-IODO-DEOXYURIDINE-MONOPHOSPHATE==
-Thymidine kinase from Herpes simplex virus type 1 (TK) was crystallized in an N-terminally truncated but fully active form. The structures of TK complexed with ADP at the ATP-site and deoxythymidine-5'-monophosphate (dTMP), deoxythymidine (dT), or idoxuridine-5'-phosphate (5-iodo-dUMP) at the substrate-site were refined to 2.75 A, 2.8 A, and 3.0 A resolution, respectively. TK catalyzes the phosphorylation of dT resulting in an ester, and the phosphorylation of dTMP giving rise to an anhydride. The presented TK structures indicate that there are only small differences between these two modes of action. Glu83 serves as a general base in the ester reaction. Arg163 parks at an internal aspartate during ester formation and binds the alpha-phosphate of dTMP during anhydride formation. The bound deoxythymidine leaves a 35 A3 cavity at position 5 of the base and two sequestered water molecules at position 2. Cavity and water molecules reduce the substrate specificity to such an extent that TK can phosphorylate various substrate analogues useful in pharmaceutical applications. TK is structurally homologous to the well-known nucleoside monophosphate kinases but contains large additional peptide segments.
+<StructureSection load='3vtk' size='340' side='right'caption='[[3vtk]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3vtk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_alphaherpesvirus_1_strain_F Human alphaherpesvirus 1 strain F]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VTK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VTK FirstGlance]. <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]] 3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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=3vtk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vtk OCA], [https://pdbe.org/3vtk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vtk RCSB], [https://www.ebi.ac.uk/pdbsum/3vtk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vtk ProSAT]</span></td></tr>
+</table>
+== Function ==
+[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).
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vt/3vtk_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3vtk ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-VTK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Human_herpesvirus_4 Human herpesvirus 4] with <scene name='pdbligand=ADP:'>ADP</scene> and <scene name='pdbligand=5IU:'>5IU</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VTK OCA].
+*[[Thymidine kinase 3D structures|Thymidine kinase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-The structures of thymidine kinase from herpes simplex virus type 1 in complex with substrates and a substrate analogue., Wild K, Bohner T, Folkers G, Schulz GE, Protein Sci. 1997 Oct;6(10):2097-106. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9336833 9336833]
+[[Category: Human alphaherpesvirus 1 strain F]]
-[[Category: Human herpesvirus 4]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Schulz GE]]
-[[Category: Thymidine kinase]]
+[[Category: Wild K]]
-[[Category: Schulz, G E.]]
-[[Category: Wild, K.]]
-[[Category: 5IU]]
-[[Category: ADP]]
-[[Category: additional thymidylate kinase activity]]
-[[Category: key enzyme in thymidine salvage pathway]]
-[[Category: target for anti-herpes viral drugs]]
-[[Category: transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:11:44 2008''