1oe0: Difference between revisions

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-[[Image:1oe0.jpg|left|200px]]<br /><applet load="1oe0" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1oe0, resolution 2.40&Aring;" />
-'''CRYSTAL STRUCTURE OF DROSOPHILA DEOXYRIBONUCLEOSIDE KINASE IN COMPLEX WITH DTTP'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF DROSOPHILA DEOXYRIBONUCLEOSIDE KINASE IN COMPLEX WITH DTTP==
-Deoxyribonucleoside kinases are feedback inhibited by the final products, of the salvage pathway, the deoxyribonucleoside triphosphates. In the, present study, the mechanism of feedback inhibition is presented based on, the crystal structure of a complex between the fruit fly, deoxyribonucleoside kinase and its feedback inhibitor deoxythymidine, triphosphate. The inhibitor was found to be bound as a bisubstrate, inhibitor with its nucleoside part in the nucleoside binding site and with, its phosphate groups partially occupying the phosphate donor site. The, overall structure of the enzyme--inhibitor complex is very similar to the, enzyme--substrate complexes with deoxythymidine and deoxycytidine, except, for a conformational change within a region otherwise directly involved in, catalysis. This conformational change involves a magnesium ion, which is, coordinated in the inhibitor complex to the phosphates and to the primary, base, Glu52, that normally is positioned close to the 5'-OH of the, substrate deoxyribose.
+<StructureSection load='1oe0' size='340' side='right'caption='[[1oe0]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1oe0]] is a 4 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=1OE0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OE0 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]] 2.4&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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=1oe0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oe0 OCA], [https://pdbe.org/1oe0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oe0 RCSB], [https://www.ebi.ac.uk/pdbsum/1oe0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oe0 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[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>
+== 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/oe/1oe0_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=1oe0 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Deoxyribonucleoside kinases are feedback inhibited by the final products of the salvage pathway, the deoxyribonucleoside triphosphates. In the present study, the mechanism of feedback inhibition is presented based on the crystal structure of a complex between the fruit fly deoxyribonucleoside kinase and its feedback inhibitor deoxythymidine triphosphate. The inhibitor was found to be bound as a bisubstrate inhibitor with its nucleoside part in the nucleoside binding site and with its phosphate groups partially occupying the phosphate donor site. The overall structure of the enzyme--inhibitor complex is very similar to the enzyme--substrate complexes with deoxythymidine and deoxycytidine, except for a conformational change within a region otherwise directly involved in catalysis. This conformational change involves a magnesium ion, which is coordinated in the inhibitor complex to the phosphates and to the primary base, Glu52, that normally is positioned close to the 5'-OH of the substrate deoxyribose.
-==About this Structure==
+Structural basis for feedback inhibition of the deoxyribonucleoside salvage pathway: studies of the Drosophila deoxyribonucleoside kinase.,Mikkelsen NE, Johansson K, Karlsson A, Knecht W, Andersen G, Piskur J, Munch-Petersen B, Eklund H Biochemistry. 2003 May 20;42(19):5706-12. PMID:12741827<ref>PMID:12741827</ref>
-OE0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster] with MG and TTP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Known structural/functional Site: <scene name='pdbsite=AC1:Mg Binding Site For Chain D'>AC1</scene>. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1OE0 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structural basis for feedback inhibition of the deoxyribonucleoside salvage pathway: studies of the Drosophila deoxyribonucleoside kinase., Mikkelsen NE, Johansson K, Karlsson A, Knecht W, Andersen G, Piskur J, Munch-Petersen B, Eklund H, Biochemistry. 2003 May 20;42(19):5706-12. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12741827 12741827]
+</div>
-[[Category: Deoxynucleoside kinase]]
+<div class="pdbe-citations 1oe0" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Drosophila melanogaster]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Andersen, G.]]
+[[Category: Andersen G]]
-[[Category: Eklund, H.]]
+[[Category: Eklund H]]
-[[Category: Johansson, K.]]
+[[Category: Johansson K]]
-[[Category: Karlsson, A.]]
+[[Category: Karlsson A]]
-[[Category: Knecht, W.]]
+[[Category: Knecht W]]
-[[Category: Mikkelsen, N.E.]]
+[[Category: Mikkelsen NE]]
-[[Category: Munch-Petersen, B.]]
+[[Category: Munch-Petersen B]]
-[[Category: Piskur, J.]]
+[[Category: Piskur J]]
-[[Category: MG]]
-[[Category: TTP]]
-[[Category: complex]]
-[[Category: deoxyribonucleoside kinase]]
-[[Category: drosophila]]
-[[Category: dttp]]
-[[Category: feedback inhibition]]
-[[Category: salvage pathway]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Dec 18 17:34:58 2007''