1zmx: Difference between revisions

Revision as of 17:49, 3 May 2008

Crystal structure of D. melanogaster deoxyribonucleoside kinase N64D mutant in complex with thymidine

OverviewOverview

The Drosophila melanogaster deoxyribonucleoside kinase (Dm-dNK) double mutant N45D/N64D was identified during a previous directed evolution study. This mutant enzyme had a decreased activity towards the natural substrates and decreased feedback inhibition with dTTP, whereas the activity with 3'-modified nucleoside analogs like 3'-azidothymidine (AZT) was nearly unchanged. Here, we identify the mutation N64D as being responsible for these changes. Furthermore, we crystallized the mutant enzyme in the presence of one of its substrates, thymidine, and the feedback inhibitor, dTTP. The introduction of the charged Asp residue appears to destabilize the LID region (residues 167-176) of the enzyme by electrostatic repulsion and no hydrogen bond to the 3'-OH is made in the substrate complex by Glu172 of the LID region. This provides a binding space for more bulky 3'-substituents like the azido group in AZT but influences negatively the interactions between Dm-dNK, substrates and feedback inhibitors based on deoxyribose. The detailed picture of the structure-function relationship provides an improved background for future development of novel mutant suicide genes for Dm-dNK-mediated gene therapy.

About this StructureAbout this Structure

1ZMX is a Single protein structure of sequence from Drosophila melanogaster. Full crystallographic information is available from OCA.

ReferenceReference

Structural basis for the changed substrate specificity of Drosophila melanogaster deoxyribonucleoside kinase mutant N64D., Welin M, Skovgaard T, Knecht W, Zhu C, Berenstein D, Munch-Petersen B, Piskur J, Eklund H, FEBS J. 2005 Jul;272(14):3733-42. PMID:16008571 Page seeded by OCA on Sat May 3 17:49:35 2008

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OCA

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 [[Image:1zmx.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 1zmx |SIZE=350|CAPTION= <scene name='initialview01'>1zmx</scene>, resolution 3.10&Aring;
+The line below this paragraph, containing "STRUCTURE_1zmx", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxynucleoside_kinase Deoxynucleoside kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.145 2.7.1.145] </span>
+or leave the SCENE parameter empty for the default display.
-|GENE= dnk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 Drosophila melanogaster])
+-->
-|DOMAIN=
+{{STRUCTURE_1zmx|  PDB=1zmx  |  SCENE=  }}
-|RELATEDENTRY=[[1j90|1J90]], [[1ot3|1OT3]], [[1oe0|1OE0]], [[1zm7|1ZM7]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1zmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zmx OCA], [http://www.ebi.ac.uk/pdbsum/1zmx PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1zmx RCSB]</span>
-}}
 '''Crystal structure of D. melanogaster deoxyribonucleoside kinase N64D mutant in complex with thymidine'''
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 [[Category: Skovgaard, T.]]
 [[Category: Welin, M.]]
-[[Category: dnk]]
+[[Category: Dnk]]
-[[Category: drosophila melanogaster]]
+[[Category: Drosophila melanogaster]]
-[[Category: n64d mutant]]
+[[Category: N64d mutant]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 17:49:35 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:38:56 2008''