1zmx

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[[Image:1zmx.gif|left|200px]]
 
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{{Structure
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==Crystal structure of D. melanogaster deoxyribonucleoside kinase N64D mutant in complex with thymidine==
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|PDB= 1zmx |SIZE=350|CAPTION= <scene name='initialview01'>1zmx</scene>, resolution 3.10&Aring;
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<StructureSection load='1zmx' size='340' side='right'caption='[[1zmx]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</scene>
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<table><tr><td colspan='2'>[[1zmx]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZMX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZMX FirstGlance]. <br>
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|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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1&#8491;</td></tr>
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|GENE= dnk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 Drosophila melanogaster])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</scene></td></tr>
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|DOMAIN=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1zmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zmx OCA], [https://pdbe.org/1zmx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zmx RCSB], [https://www.ebi.ac.uk/pdbsum/1zmx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zmx ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1j90|1J90]], [[1ot3|1OT3]], [[1oe0|1OE0]], [[1zm7|1ZM7]]
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</table>
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|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>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/DNK_DROME DNK_DROME] Deoxyribonucleoside kinase that has a broad specificity phosphorylating thymidine, deoxyadenosine, deoxycytidine and deoxyguanosine. Specificity is higher for pyrimidine nucleosides. Several anti-viral and anti-cancer nucleoside analogs are also efficiently phosphorylated.<ref>PMID:10446143</ref> <ref>PMID:10692477</ref> <ref>PMID:16008571</ref>
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== Evolutionary Conservation ==
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'''Crystal structure of D. melanogaster deoxyribonucleoside kinase N64D mutant in complex with thymidine'''
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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==Overview==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zm/1zmx_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1zmx ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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.
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.
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==About this Structure==
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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<ref>PMID:16008571</ref>
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1ZMX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZMX OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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:[http://www.ncbi.nlm.nih.gov/pubmed/16008571 16008571]
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</div>
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[[Category: Deoxynucleoside kinase]]
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<div class="pdbe-citations 1zmx" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Drosophila melanogaster]]
[[Category: Drosophila melanogaster]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Berenstein, D.]]
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[[Category: Berenstein D]]
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[[Category: Eklund, H.]]
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[[Category: Eklund H]]
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[[Category: Knecht, W.]]
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[[Category: Knecht W]]
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[[Category: Munch-Petersen, B.]]
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[[Category: Munch-Petersen B]]
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[[Category: Piskur, J.]]
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[[Category: Piskur J]]
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[[Category: Skovgaard, T.]]
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[[Category: Skovgaard T]]
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[[Category: Welin, M.]]
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[[Category: Welin M]]
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[[Category: dnk]]
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[[Category: drosophila melanogaster]]
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[[Category: n64d mutant]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:38:56 2008''
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Current revision

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

PDB ID 1zmx

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