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.


1e2h

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "1e2h" [edit=sysop:move=sysop])
Current revision (08:10, 6 December 2023) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1e2h.png|left|200px]]
 
-
<!--
+
==The nucleoside binding site of Herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography==
-
The line below this paragraph, containing "STRUCTURE_1e2h", creates the "Structure Box" on the page.
+
<StructureSection load='1e2h' size='340' side='right'caption='[[1e2h]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[1e2h]] 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=1E2H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E2H FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
{{STRUCTURE_1e2h| PDB=1e2h | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1e2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e2h OCA], [https://pdbe.org/1e2h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e2h RCSB], [https://www.ebi.ac.uk/pdbsum/1e2h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e2h 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/e2/1e2h_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=1e2h ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The crystal structures of the full-length Herpes simplex virus type 1 thymidine kinase in its unligated form and in a complex with an adenine analogue have been determined at 1.9 A resolution. The unligated enzyme contains four water molecules in the thymidine pocket and reveals a small induced fit on substrate binding. The structure of the ligated enzyme shows for the first time a bound adenine analogue after numerous complexes with thymine and guanine analogues have been reported. The adenine analogue constitutes a new lead compound for enzyme-prodrug gene therapy. In addition, the structure of mutant Q125N modifying the binding site of the natural substrate thymidine in complex with this substrate has been established at 2.5 A resolution. It reveals that neither the binding mode of thymidine nor the polypeptide backbone conformation is altered, except that the two major hydrogen bonds to thymidine are replaced by a single water-mediated hydrogen bond, which improves the relative acceptance of the prodrugs aciclovir and ganciclovir compared with the natural substrate. Accordingly, the mutant structure represents a first step toward improving the virus-directed enzyme-prodrug gene therapy by enzyme engineering.
-
===THE NUCLEOSIDE BINDING SITE OF HERPES SIMPLEX TYPE 1 THYMIDINE KINASE ANALYZED BY X-RAY CRYSTALLOGRAPHY===
+
Nucleoside binding site of herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography.,Vogt J, Perozzo R, Pautsch A, Prota A, Schelling P, Pilger B, Folkers G, Scapozza L, Schulz GE Proteins. 2000 Dec 1;41(4):545-53. PMID:11056041<ref>PMID:11056041</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_11056041}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 1e2h" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 11056041 is the PubMed ID number.
+
-
-->
+
-
{{ABSTRACT_PUBMED_11056041}}
+
-
 
+
-
==About this Structure==
+
-
[[1e2h]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Viruses Viruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E2H OCA].
+
==See Also==
==See Also==
-
*[[Herpes Simplex Virus Thymidine Kinase]]
+
*[[Thymidine kinase 3D structures|Thymidine kinase 3D structures]]
-
 
+
== References ==
-
==Reference==
+
<references/>
-
<ref group="xtra">PMID:11056041</ref><ref group="xtra">PMID:7628623</ref><ref group="xtra">PMID:7552712</ref><references group="xtra"/>
+
__TOC__
-
[[Category: Thymidine kinase]]
+
</StructureSection>
-
[[Category: Viruses]]
+
[[Category: Human alphaherpesvirus 1 strain 17]]
-
[[Category: Scapozza, L.]]
+
[[Category: Large Structures]]
-
[[Category: Schulz, G E.]]
+
[[Category: Scapozza L]]
-
[[Category: Vogt, J.]]
+
[[Category: Schulz GE]]
-
[[Category: Adenine analog]]
+
[[Category: Vogt J]]
-
[[Category: Enzyme-prodrug gene therapy]]
+
-
[[Category: Nucleoside- binding]]
+
-
[[Category: Thymidine kinase]]
+
-
[[Category: Transferase]]
+
-
[[Category: X-ray crystallography]]
+

Current revision

The nucleoside binding site of Herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography

PDB ID 1e2h

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/1e2h"
Personal tools